[2024-01-25 17:53:50,392] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference
[2024-01-25 17:53:51,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,536] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d0352c3-9b5d-4e7f-be5b-76c44593f661/GCF_003752155.1_ASM375215v1_genomic.fna.gz | prodigal -d GCF_003752155.1_ASM375215v1_genomic.fna/cds.fna -a GCF_003752155.1_ASM375215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:58,703] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:58,703] [INFO] Task started: HMMsearch
[2024-01-25 17:53:58,703] [INFO] Running command: hmmsearch --tblout GCF_003752155.1_ASM375215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference/reference_markers.hmm GCF_003752155.1_ASM375215v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:58,967] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:58,968] [INFO] Found 6/6 markers.
[2024-01-25 17:53:58,998] [INFO] Query marker FASTA was written to GCF_003752155.1_ASM375215v1_genomic.fna/markers.fasta
[2024-01-25 17:53:58,999] [INFO] Task started: Blastn
[2024-01-25 17:53:58,999] [INFO] Running command: blastn -query GCF_003752155.1_ASM375215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference/reference_markers.fasta -out GCF_003752155.1_ASM375215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:59,576] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:59,578] [INFO] Selected 24 target genomes.
[2024-01-25 17:53:59,579] [INFO] Target genome list was writen to GCF_003752155.1_ASM375215v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:59,586] [INFO] Task started: fastANI
[2024-01-25 17:53:59,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d0352c3-9b5d-4e7f-be5b-76c44593f661/GCF_003752155.1_ASM375215v1_genomic.fna.gz --refList GCF_003752155.1_ASM375215v1_genomic.fna/target_genomes.txt --output GCF_003752155.1_ASM375215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:15,461] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:15,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:15,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:15,470] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:15,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:15,470] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	100.0	1332	1334	95	conclusive
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	77.807	110	1334	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	77.7039	127	1334	95	below_threshold
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	77.6416	173	1334	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	77.4147	169	1334	95	below_threshold
Anaerocolumna cellulosilytica	strain=SN021	GCA_014218335.1	433286	433286	type	True	77.1995	105	1334	95	below_threshold
Anaerocolumna cellulosilytica	strain=DSM 100423	GCA_014202875.1	433286	433286	type	True	77.1194	101	1334	95	below_threshold
[Clostridium] polysaccharolyticum	strain=DSM 1801	GCA_900111595.1	29364	29364	type	True	76.9667	85	1334	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	76.9517	100	1334	95	below_threshold
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	76.9501	97	1334	95	below_threshold
Variimorphobacter saccharofermentans	strain=MD1	GCA_014174405.1	2755051	2755051	type	True	76.867	73	1334	95	below_threshold
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	76.2401	56	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:15,472] [INFO] DFAST Taxonomy check result was written to GCF_003752155.1_ASM375215v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:15,473] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:15,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:15,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference/checkm_data
[2024-01-25 17:54:15,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:15,514] [INFO] Task started: CheckM
[2024-01-25 17:54:15,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003752155.1_ASM375215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003752155.1_ASM375215v1_genomic.fna/checkm_input GCF_003752155.1_ASM375215v1_genomic.fna/checkm_result
[2024-01-25 17:54:40,954] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:40,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:40,976] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:40,976] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:40,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003752155.1_ASM375215v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:40,977] [INFO] Task started: Blastn
[2024-01-25 17:54:40,977] [INFO] Running command: blastn -query GCF_003752155.1_ASM375215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae485fe-5454-4f51-a07e-21bcc042ae81/dqc_reference/reference_markers_gtdb.fasta -out GCF_003752155.1_ASM375215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:42,024] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:42,029] [INFO] Selected 21 target genomes.
[2024-01-25 17:54:42,029] [INFO] Target genome list was writen to GCF_003752155.1_ASM375215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:42,046] [INFO] Task started: fastANI
[2024-01-25 17:54:42,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d0352c3-9b5d-4e7f-be5b-76c44593f661/GCF_003752155.1_ASM375215v1_genomic.fna.gz --refList GCF_003752155.1_ASM375215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003752155.1_ASM375215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:59,334] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:59,345] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:59,345] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003752155.1	s__Mobilisporobacter senegalensis	100.0	1332	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilisporobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012070565.1	s__Anaerosporobacter sp012070565	77.8149	109	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142955.1	s__Anaerosporobacter mobilis	77.6721	129	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	77.6203	175	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018372435.1	s__Anaerosporobacter sp018372435	77.5403	123	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	96.90	96.04	0.88	0.87	3	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	77.4147	169	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCA_009731425.1	s__KM106-2 sp009731425	77.2831	116	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KM106-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218335.1	s__Anaerocolumna cellulosilytica	77.2404	107	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014218355.1	s__Anaerocolumna sp014218355	77.0646	94	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733755.1	s__Lachnoclostridium phytofermentans_A	77.0276	85	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	99.72	99.18	0.93	0.85	4	-
GCF_900111595.1	s__Clostridium_AI polysaccharolyticum	76.9667	85	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786205.1	s__CAG-411 sp902786205	76.6607	70	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539655.1	s__Robinsoniella sp900539655	76.6256	59	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.96	99.96	0.92	0.92	2	-
GCF_018918265.1	s__Falcatimonas sp018918265	76.6075	71	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_018365455.1	s__Robinsoniella sp900555455	76.4394	68	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.95	99.95	0.97	0.97	2	-
GCA_002434335.1	s__Anaerocolumna sp002434335	76.3584	91	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.22	99.22	0.91	0.91	2	-
GCA_000875945.1	s__TWA4 sp000875945	76.3168	52	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TWA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900045905.1	s__Fimimorpha sp900045905	76.2045	67	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fimimorpha	95.0	97.84	97.84	0.82	0.82	2	-
GCA_910585935.1	s__MGBC136627 sp910585935	76.1602	58	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MGBC136627	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:59,347] [INFO] GTDB search result was written to GCF_003752155.1_ASM375215v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:59,347] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:59,350] [INFO] DFAST_QC result json was written to GCF_003752155.1_ASM375215v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:59,350] [INFO] DFAST_QC completed!
[2024-01-25 17:54:59,350] [INFO] Total running time: 0h1m9s