[2023-06-29 15:15:16,468] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:15:16,470] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:15:16,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference
[2023-06-29 15:15:17,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:15:17,742] [INFO] Task started: Prodigal
[2023-06-29 15:15:17,742] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3330ee0-d141-4f02-abb0-558a9bfbede5/GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:15:23,167] [INFO] Task succeeded: Prodigal
[2023-06-29 15:15:23,167] [INFO] Task started: HMMsearch
[2023-06-29 15:15:23,167] [INFO] Running command: hmmsearch --tblout GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference/reference_markers.hmm GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:15:23,409] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:15:23,410] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3330ee0-d141-4f02-abb0-558a9bfbede5/GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 15:15:23,438] [INFO] Query marker FASTA was written to GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 15:15:23,439] [INFO] Task started: Blastn
[2023-06-29 15:15:23,439] [INFO] Running command: blastn -query GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference/reference_markers.fasta -out GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:15:24,114] [INFO] Task succeeded: Blastn
[2023-06-29 15:15:24,118] [INFO] Selected 7 target genomes.
[2023-06-29 15:15:24,119] [INFO] Target genome list was writen to GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 15:15:24,120] [INFO] Task started: fastANI
[2023-06-29 15:15:24,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3330ee0-d141-4f02-abb0-558a9bfbede5/GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:15:28,023] [INFO] Task succeeded: fastANI
[2023-06-29 15:15:28,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:15:28,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:15:28,035] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:15:28,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:15:28,035] [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
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	84.5973	402	523	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	82.5545	371	523	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	82.4751	366	523	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	81.9022	340	523	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.2688	262	523	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.0164	123	523	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.6183	133	523	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:15:28,038] [INFO] DFAST Taxonomy check result was written to GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 15:15:28,038] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:15:28,039] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:15:28,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference/checkm_data
[2023-06-29 15:15:28,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:15:28,061] [INFO] Task started: CheckM
[2023-06-29 15:15:28,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 15:15:50,039] [INFO] Task succeeded: CheckM
[2023-06-29 15:15:50,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:15:50,081] [INFO] ===== Completeness check finished =====
[2023-06-29 15:15:50,081] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:15:50,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 15:15:50,082] [INFO] Task started: Blastn
[2023-06-29 15:15:50,082] [INFO] Running command: blastn -query GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg055ece47-6c59-4878-8967-113e3e46b0b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:15:51,165] [INFO] Task succeeded: Blastn
[2023-06-29 15:15:51,171] [INFO] Selected 12 target genomes.
[2023-06-29 15:15:51,171] [INFO] Target genome list was writen to GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:15:51,174] [INFO] Task started: fastANI
[2023-06-29 15:15:51,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3330ee0-d141-4f02-abb0-558a9bfbede5/GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:15:57,105] [INFO] Task succeeded: fastANI
[2023-06-29 15:15:57,121] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:15:57,121] [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_004558805.1	s__Faecalibacterium prausnitzii_M	98.0137	473	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.98	97.83	0.94	0.93	3	conclusive
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	84.6926	396	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCA_900772565.1	s__Faecalibacterium sp900772565	84.6868	366	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	84.5349	405	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCA_900539945.1	s__Faecalibacterium sp900539945	84.4669	389	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	84.0699	403	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCA_003449675.1	s__Faecalibacterium sp003449675	83.9057	288	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCA_900539885.1	s__Faecalibacterium sp900539885	83.8517	375	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	83.8262	393	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCF_002549755.1	s__Faecalibacterium prausnitzii_D	83.579	389	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.37	96.64	0.86	0.78	38	-
GCA_905215595.1	s__Faecalibacterium sp905215595	83.4743	320	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765105.1	s__Faecalibacterium sp900765105	83.0216	315	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-29 15:15:57,123] [INFO] GTDB search result was written to GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 15:15:57,124] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:15:57,131] [INFO] DFAST_QC result json was written to GCA_937968665.1_SRR3992983_bin.13_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 15:15:57,131] [INFO] DFAST_QC completed!
[2023-06-29 15:15:57,131] [INFO] Total running time: 0h0m41s