Silent output #35
Description
Hello,
I am executing annotate_rm and it seems to exit OK but the output folder remains empty. Please see below:
⬢ [Systemd] >MicrobeMod annotate_rm -f final_mags/metagenome_assembly.fna -o final_mageval/microbemod_assembly/ -t 20
25-02-24 12:19:30 INFO Calling prodigal on FASTA file: final_mags/metagenome_assembly.fna
25-02-24 12:19:30 INFO Running prodigal: prodigal -i final_mags/metagenome_assembly.fna -a final_mageval/microbemod_assembly/.faa
25-02-24 13:16:02 INFO Running HMMER: hmmsearch --cut_ga --cpu 20 --domtblout final_mageval/microbemod_assembly/.hits /researchdrive/gkanaan/tools/MicrobeMod/MicrobeMod/db/HMMs/RM_HMMs.hmm final_mageval/microbemod_assembly/.faa
25-02-24 13:39:03 INFO Running cath: cath-resolve-hits --input-format hmmer_domtblout final_mageval/microbemod_assembly/.hits --hits-text-to-file final_mageval/microbemod_assembly/.resolved.hits
25-02-24 13:39:47 INFO Running BLASTP against REBASE: blastp -query final_mageval/microbemod_assembly/.rm.genes.faa -db /researchdrive/gkanaan/tools/MicrobeMod/MicrobeMod/db/rebase_blast/all_rebase_proteins.faa -outfmt 6 -evalue 1e-5 -num_threads 20 > final_mageval/microbemod_assembly/.blast
⬢ [Systemd] > ls -la final_mageval/microbemod_assembly/
total 1223769
drwxrwxr-x 2 gkanaan gkanaan 8 Feb 24 13:53 .
drwxrwxr-x 7 gkanaan gkanaan 8 Feb 24 12:19 ..
-rw-rw-r-- 1 gkanaan gkanaan 66983548 Feb 24 13:53 .blast
-rw-rw-r-- 1 gkanaan gkanaan 1180995006 Feb 24 13:15 .faa
-rw-rw-r-- 1 gkanaan gkanaan 2752745 Feb 24 13:39 .hits
-rw-rw-r-- 1 gkanaan gkanaan 205665 Feb 24 13:39 .resolved.hits
-rw-rw-r-- 1 gkanaan gkanaan 741640 Feb 24 13:39 .rm.genes.faa
-rw-rw-r-- 1 gkanaan gkanaan 135204 Feb 24 13:53 .rm.genes.tsv
Here is the head of each file:
==> .resolved.hits <==
# Generated by cath-resolve-hits v0.16.10-0-g99edb28, one of the cath-tools (https://github.com/UCLOrengoGroup/cath-tools)
#FIELDS query-id match-id score boundaries resolved cond-evalue indp-evalue
c_000000000091_5 Methyltransf_25 37.6 117-215 117-215 1.5e-10 7.7e-07
c_000000000136_36 Type_II_MTases_FAM_2 48 5-189 5-189 3.2e-14 2.9e-10
c_000000000282_120 Type_I_REases_FAM_2.einsi_trimmed 353.2 1-403 1-403 3.3e-107 9.4e-103
c_000000000282_121 Type_I_REases_FAM_2.einsi_trimmed 62.5 5-96 5-96 2.4e-19 6.8e-15
c_000000000282_131 Type_II_MTases_FAM_33 22.9 2-60 2-60 2.8e-07 0.009
c_000000000282_132 Type_II_MTases_FAM_33 54.1 10-111 10-111 9.7e-17 3.1e-12
c_000000000282_2 Type_I_REases_FAM_0.einsi_trimmed 76.8 16-93 16-93 7.2e-24 3.2e-19
c_000000000282_3 Type_I_REases_FAM_0.einsi_trimmed 98.2 1-140 1-140 2.7e-30 1.2e-25
==> .rm.genes.faa <==
>c_000000000136_36 # 17288 # 17899 # -1 # ID=133_36;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.426
MEFEYQDGVYETKQRVYSENGKSPTLTAGNKEQYIETHNKPEQVGTAVDIKGHDQIKRVYSPNGKSPTVTTCGGGHREPKVVSGAWRARSVDENGKRVDWKETTPQQMLELRKDEKTNSVTSVQKDNVLTKNNVYWRKLTPLECMRLQTVQDDYLMPVSNTQKYKILGNGWTIEVIAHIFENMKLLEDGKDLPKPKGQDTFDF*
>c_000000000282_2 # 714 # 1127 # 1 # ID=275_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399
MLLLNETHKVHDGASALSSTYATEALIQQVISAPLQVGSHKTHHVWHTTGSGKTLTSFKTSQILMDLPAVYKVVFVVDRKDLDYQTMQELGLLLRMVVLILLIIPTAWSISSWVSLKIKEGAAKRFRPNHYHHTKTK*
>c_000000000282_3 # 1264 # 1710 # 1 # ID=275_3;partial=00;start_type=TTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.371
MFGFTGTPIFADNASKNDLGKRTTKDLFGNCLHKYVITDAISDENVLKFGIEYYSVFKHKNKPQFDEMVEDINKEEVFNDPKYLEGVANYIIANHNRKTFNKDYSALFAVSSIDAAIAYYGVVSTKEVSRRARFAYCNHFHLWRKRRR*
>c_000000000282_4 # 1689 # 2174 # 1 # ID=275_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.360
MAQTKTVKKPRIISLMKSLVWLPNLKLVYQSSHTRDKLESFIGDYNQMYQTSYTTKDSKLFEGYFKDISKRLKEREKQNFNDEKDRLDIVIVVNMMLTGFDAKKVNTLYVDKNLKQHGLIQAFSRTNRILGEQKSQGNMLCLETLKKLQMMPLLCFLIKRR*
>c_000000000282_120 # 116838 # 118052 # -1 # ID=275_120;partial=00;start_type=TTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.336
MANSNPDIAGRPYQIEAIKRVSDSFVVKGEDGIRGGMRNALLVMATGSGKTRTAAAMVDVLFKNNWVKRVLFLADRNALVRQAKKNFGEHLKELTSVNLSEDKEQDEVRLVFSTYPTMMNRIDSIRNSDERFYGVGHFDLIIVDEAHRSVYNRYKSIFDYFDSLVVGLTATPKESIDHNTFELFGCPTKDPTFNYDLEQAVPTYLNPFKNFDISTSFLREGIKYNELSDEEKVKYEATFTDKATGLFPEEIEASKMNKKLFNIDTVNKVLDAVMENGLKIEGGDKLGRTIIFAVNQNHAKFIVECFEKRYPDKPSGFIAMIHNDVSHAQSLIDSFCDHFKENNPQIAVSVDMMDTGIDAPRVLNLVFFKVVRSYAKFWQMIGRGTRLCPDVFRPNQPKRRVFNF*
==> .rm.genes.tsv <==
Operon Gene System Type Gene type HMM Evalue REBASE homolog Homolog identity(%) Homolog methylation Homolog motif
RM Operon #1 c_000000000282_120 RM_Type_I RE Type_I_REases_FAM_2.einsi_trimmed 9.4e-103 FenDK69ORF12900P 77.475
RM Operon #1 c_000000000282_121 RM_Type_I RE Type_I_REases_FAM_2.einsi_trimmed 6.8e-15 FspM31R6ORF9355P 89.286
RM Operon #1 c_000000000282_132 RM_Type_II MT Type_II_MTases_FAM_33 3.1e-12 M.Mtr4126ORF1391P 59.13 m6A
RM Operon #1 c_000000000282_131 RM_Type_II MT Type_II_MTases_FAM_33 0.009 M.PspJZB09ORFAP 79.661 m6A
RM Operon #10 c_000000009740_13 RM_Type_II MT Type_II_MTases_FAM_0 6.6e-53 M.SspYLB08ORF3315P 79.962 m5C
RM Operon #10 c_000000009740_15 RM_Type_II RE Type_II_REase21 1.7e-20 PaqP86ORF18270P 80.11
RM Operon #100 c_000000081936_1 RM_Type_IIG IIG Type_IIG_FAM_1.einsi_trimmed 2.2e-89 Rso909ORFBP 55.814 m6A
RM Operon #101 c_000000082091_8 RM_Type_I SP Type_I_S_51 6.5e-104
RM Operon #101 c_000000082091_9 RM_Type_I MT Type_I_MTases_FAM_0 5.1e-165 M.LspA80ORF13005P 92.308 m6A
==> .faa <==
>c_000000000001_1 # 2 # 292 # -1 # ID=1_1;partial=10;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.543
MRSLRRGLLLLLYYFSTLELRQFDFYERAVVHRVEAGPSRMSWCYFAPPHRAGAYTASRR
FRPGKVQIGPRQVLGPYGRTYEPTCHIGDLGYSSSWT
>c_000000000001_2 # 335 # 616 # -1 # ID=1_2;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.621
MDSLPGEPPGGGGGVRGSLGGGNLGGGFGGRGDLGGCFGGGSGAGAGGRRLTREEGLERG
HLFLEGARACCFFRQALFFVFRGLGSLNFDHEF*
>c_000000000001_3 # 571 # 948 # -1 # ID=1_3;partial=00;start_type=GTG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.730
MPAAAGGVKGKEEGGKVRRAVAGGAGGEGGGKGREVGAPPPNQREGGGCGPWKRTHPGGS
GGGRAGGGRDKVLLWLRPGQYLMVKLRGAQYPARADPPLGIGALGVREVRGWIVCQGSLL
GVGEG*
==> .hits <==
# --- full sequence --- -------------- this domain ------------- hmm coord ali
coord env coord
# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from
to from to acc description of target
#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- -----
----- ----- ----- ---- ---------------------
c_000000071267_64 - 213 PCMT PF01135.23 210 1.1e-65 229.3 0.0 1 1 5.9e-70 1.4e-65 229.0 0.0 4 207 9
208 6 210 0.96 # 63961 # 64599 # -1 # ID=69028_64;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.382
c_000000022658_63 - 213 PCMT PF01135.23 210 3e-63 221.4 0.0 1 1 1.6e-67 3.8e-63 221.0 0.0 6 206 11
207 6 210 0.95 # 42224 # 42862 # -1 # ID=21991_63;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.427
c_000000083169_61 - 226 PCMT PF01135.23 210 1.6e-61 215.8 0.0 1 1 8.7e-66 2.1e-61 215.3 0.0 6 206 25
220 20 223 0.95 # 63137 # 63814 # -1 # ID=80047_61;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.453
c_000000010713_99 - 230 PCMT PF01135.23 210 1.9e-61 215.5 0.0 1 1 9.7e-66 2.3e-61 215.2 0.0 3 206 25
223 22 226 0.97 # 100190 # 100879 # -1 # ID=10371_99;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.586
c_000000003666_30 - 215 PCMT PF01135.23 210 4.3e-61 214.3 0.0 1 1 2.1e-65 5e-61 214.1 0.0 5 208 10
209 6 211 0.98 # 24487 # 25131 # 1 # ID=3548_30;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.665
c_000000075496_219 - 222 PCMT PF01135.23 210 1.6e-57 202.6 0.0 1 1 8.2e-62 2e-57 202.4 0.0 3 205 17
214 14 219 0.97 # 224810 # 225475 # -1 # ID=72906_219;partial=00;start_type=GTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.450
c_000000078609_256 - 214 PCMT PF01135.23 210 5.2e-56 197.7 0.0 1 1 2.5e-60 6.1e-56 197.5 0.0 4 208 12
211 8 213 0.95 # 268546 # 269187 # -1 # ID=75812_256;partial=00;start_type=TTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.394
==> .blast <==
c_000000000136_36 REBASE:M.EsaSS1405ORFAP-putative_Type_II_methyltransferase-m5C-GATC 56.463 147 55 6 43 183 3 146 3.82e-46 153
c_000000000136_36 REBASE:M.EsaSS136ORFAP-putative_Type_II_methyltransferase-m5C-GATC 52.353 170 64 7 28 183 184 350 1.71e-45 157
c_000000000136_36 REBASE:M.Uph13359ORFSP-putative_Type_II_methyltransferase-m5C-GATC 40.526 190 56 5 2 183 314 454 1.37e-33 128
c_000000000136_36 REBASE:M.Uph13541ORFAP-putative_Type_II_methyltransferase-m5C-GATC 40.526 190 56 5 2 183 313 453 3.00e-33 127
c_000000000136_36 REBASE:M.EsaSS1413ORFAP-putative_Type_II_methyltransferase-m5C-GATC 45.926 135 69 4 17 149 186 318 1.59e-28 112
c_000000000136_36 REBASE:M.Uph13359ORFN2P-putative_Type_II_methyltransferase-m5C-GATC 43.275 171 40 6 22 184 218 339 1.78e-27 109
c_000000000136_36 REBASE:M2.Pvu366ORF10780P-putative_Type_II_methyltransferase-m5C- 43.262 141 70 3 43 181 46 178 2.43e-27 106
c_000000000136_36 REBASE:M1.Pte782ORFDP-putative_Type_II_methyltransferase-m5C- 43.972 141 69 3 43 181 234 366 4.62e-27 109
c_000000000136_36 REBASE:M.PcoT60ORF6305P-putative_Type_II_methyltransferase-m5C- 42.857 140 54 4 43 181 285 399 5.33e-26 107
c_000000000136_36 REBASE:M2.Pvu26ORF1835P-putative_Type_II_methyltransferase-m5C- 42.857 140 54 4 43 181 285 399 5.49e-26 107
Any tips?