[2023-06-18 23:17:32,744] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:17:32,747] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:17:32,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference
[2023-06-18 23:17:34,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:17:34,261] [INFO] Task started: Prodigal
[2023-06-18 23:17:34,261] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdca4e7d-749f-430a-9b67-3b57a1fe7dbd/GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:17:40,765] [INFO] Task succeeded: Prodigal
[2023-06-18 23:17:40,765] [INFO] Task started: HMMsearch
[2023-06-18 23:17:40,765] [INFO] Running command: hmmsearch --tblout GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference/reference_markers.hmm GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:17:41,015] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:17:41,016] [INFO] Found 6/6 markers.
[2023-06-18 23:17:41,059] [INFO] Query marker FASTA was written to GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 23:17:41,060] [INFO] Task started: Blastn
[2023-06-18 23:17:41,060] [INFO] Running command: blastn -query GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference/reference_markers.fasta -out GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:17:41,796] [INFO] Task succeeded: Blastn
[2023-06-18 23:17:41,799] [INFO] Selected 14 target genomes.
[2023-06-18 23:17:41,799] [INFO] Target genome list was writen to GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 23:17:41,800] [INFO] Task started: fastANI
[2023-06-18 23:17:41,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdca4e7d-749f-430a-9b67-3b57a1fe7dbd/GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:17:48,928] [INFO] Task succeeded: fastANI
[2023-06-18 23:17:48,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:17:48,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:17:48,939] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:17:48,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 23:17:48,940] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	84.0496	413	712	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	81.877	301	712	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.1694	248	712	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.9494	202	712	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.3552	146	712	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.0501	177	712	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.9116	190	712	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.9092	123	712	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.834	134	712	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.7177	139	712	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.2827	96	712	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.8493	98	712	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:17:48,942] [INFO] DFAST Taxonomy check result was written to GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 23:17:48,942] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:17:48,942] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:17:48,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference/checkm_data
[2023-06-18 23:17:48,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:17:48,969] [INFO] Task started: CheckM
[2023-06-18 23:17:48,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 23:18:14,762] [INFO] Task succeeded: CheckM
[2023-06-18 23:18:14,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 23:18:14,787] [INFO] ===== Completeness check finished =====
[2023-06-18 23:18:14,788] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:18:14,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 23:18:14,789] [INFO] Task started: Blastn
[2023-06-18 23:18:14,789] [INFO] Running command: blastn -query GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d04e52e-5335-4c0b-b9ee-6f9cc72a6773/dqc_reference/reference_markers_gtdb.fasta -out GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:16,145] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:16,149] [INFO] Selected 15 target genomes.
[2023-06-18 23:18:16,150] [INFO] Target genome list was writen to GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:18:16,152] [INFO] Task started: fastANI
[2023-06-18 23:18:16,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdca4e7d-749f-430a-9b67-3b57a1fe7dbd/GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:18:22,757] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:22,776] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:18:22,776] [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
GCA_018228685.1	s__CAG-83 sp001916855	97.975	634	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	conclusive
GCA_000435975.1	s__CAG-83 sp000435975	90.9569	454	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	-
GCF_018408575.1	s__CAG-83 sp000431575	84.0012	416	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	-
GCA_900551355.1	s__CAG-83 sp900551355	82.6319	253	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_902388735.1	s__CAG-83 sp902388735	82.0331	286	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCA_900547745.1	s__CAG-83 sp900547745	81.9628	309	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900545585.1	s__CAG-83 sp900545585	81.8919	324	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_900545495.1	s__CAG-83 sp900545495	81.8468	316	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900550585.1	s__CAG-83 sp900550585	81.6388	297	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900552725.1	s__CAG-83 sp900552725	81.565	286	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.50	98.05	0.78	0.74	4	-
GCA_900554275.1	s__CAG-83 sp900554275	81.3035	273	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_015068325.1	s__CAG-83 sp015068325	80.6186	264	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552475.1	s__CAG-83 sp900552475	79.8494	260	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.74	98.42	0.88	0.85	4	-
GCA_017415775.1	s__CAG-83 sp017415775	79.8098	200	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210385.1	s__Enterenecus sp905210385	77.9074	85	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:18:22,783] [INFO] GTDB search result was written to GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 23:18:22,787] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:18:22,796] [INFO] DFAST_QC result json was written to GCA_937949925.1_SRR7721894_bin.34_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 23:18:22,796] [INFO] DFAST_QC completed!
[2023-06-18 23:18:22,796] [INFO] Total running time: 0h0m50s