[2023-06-29 12:45:40,579] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:45:40,591] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:45:40,591] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference
[2023-06-29 12:45:41,900] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:45:41,901] [INFO] Task started: Prodigal
[2023-06-29 12:45:41,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg6839835d-7c68-41a3-833b-207abdefa46c/GCA_023708365.1_ASM2370836v1_genomic.fna.gz | prodigal -d GCA_023708365.1_ASM2370836v1_genomic.fna/cds.fna -a GCA_023708365.1_ASM2370836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:45:50,361] [INFO] Task succeeded: Prodigal
[2023-06-29 12:45:50,361] [INFO] Task started: HMMsearch
[2023-06-29 12:45:50,361] [INFO] Running command: hmmsearch --tblout GCA_023708365.1_ASM2370836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference/reference_markers.hmm GCA_023708365.1_ASM2370836v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:45:50,615] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:45:50,617] [INFO] Found 6/6 markers.
[2023-06-29 12:45:50,672] [INFO] Query marker FASTA was written to GCA_023708365.1_ASM2370836v1_genomic.fna/markers.fasta
[2023-06-29 12:45:50,672] [INFO] Task started: Blastn
[2023-06-29 12:45:50,672] [INFO] Running command: blastn -query GCA_023708365.1_ASM2370836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference/reference_markers.fasta -out GCA_023708365.1_ASM2370836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:45:51,415] [INFO] Task succeeded: Blastn
[2023-06-29 12:45:51,419] [INFO] Selected 7 target genomes.
[2023-06-29 12:45:51,419] [INFO] Target genome list was writen to GCA_023708365.1_ASM2370836v1_genomic.fna/target_genomes.txt
[2023-06-29 12:45:51,420] [INFO] Task started: fastANI
[2023-06-29 12:45:51,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg6839835d-7c68-41a3-833b-207abdefa46c/GCA_023708365.1_ASM2370836v1_genomic.fna.gz --refList GCA_023708365.1_ASM2370836v1_genomic.fna/target_genomes.txt --output GCA_023708365.1_ASM2370836v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:45:56,324] [INFO] Task succeeded: fastANI
[2023-06-29 12:45:56,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:45:56,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:45:56,337] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:45:56,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:45:56,338] [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	87.0514	649	871	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	85.273	583	871	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	85.2249	595	871	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	84.8905	585	871	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.8311	388	871	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.805	219	871	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.5992	55	871	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:45:56,340] [INFO] DFAST Taxonomy check result was written to GCA_023708365.1_ASM2370836v1_genomic.fna/tc_result.tsv
[2023-06-29 12:45:56,340] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:45:56,341] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:45:56,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference/checkm_data
[2023-06-29 12:45:56,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:45:56,374] [INFO] Task started: CheckM
[2023-06-29 12:45:56,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708365.1_ASM2370836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708365.1_ASM2370836v1_genomic.fna/checkm_input GCA_023708365.1_ASM2370836v1_genomic.fna/checkm_result
[2023-06-29 12:46:25,990] [INFO] Task succeeded: CheckM
[2023-06-29 12:46:25,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:46:26,013] [INFO] ===== Completeness check finished =====
[2023-06-29 12:46:26,013] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:46:26,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708365.1_ASM2370836v1_genomic.fna/markers.fasta)
[2023-06-29 12:46:26,014] [INFO] Task started: Blastn
[2023-06-29 12:46:26,014] [INFO] Running command: blastn -query GCA_023708365.1_ASM2370836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf81f57e-5229-49c0-bfa4-559c5d55b83a/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708365.1_ASM2370836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:46:27,229] [INFO] Task succeeded: Blastn
[2023-06-29 12:46:27,234] [INFO] Selected 10 target genomes.
[2023-06-29 12:46:27,234] [INFO] Target genome list was writen to GCA_023708365.1_ASM2370836v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:46:27,236] [INFO] Task started: fastANI
[2023-06-29 12:46:27,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg6839835d-7c68-41a3-833b-207abdefa46c/GCA_023708365.1_ASM2370836v1_genomic.fna.gz --refList GCA_023708365.1_ASM2370836v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708365.1_ASM2370836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:46:34,196] [INFO] Task succeeded: fastANI
[2023-06-29 12:46:34,209] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:46:34,210] [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_002549755.1	s__Faecalibacterium prausnitzii_D	96.9838	713	871	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.37	96.64	0.86	0.78	38	conclusive
GCA_900539885.1	s__Faecalibacterium sp900539885	92.6477	635	871	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	88.706	655	871	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_003324185.1	s__Faecalibacterium prausnitzii	87.0301	650	871	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	86.8156	581	871	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_003287405.1	s__Faecalibacterium prausnitzii_J	86.7478	620	871	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_900765105.1	s__Faecalibacterium sp900765105	86.7188	451	871	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
GCA_905215595.1	s__Faecalibacterium sp905215595	85.8478	447	871	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_003449675.1	s__Faecalibacterium sp003449675	85.707	412	871	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCF_010509575.1	s__Faecalibacterium prausnitzii_C	85.2588	593	871	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.30	96.44	0.84	0.71	49	-
--------------------------------------------------------------------------------
[2023-06-29 12:46:34,212] [INFO] GTDB search result was written to GCA_023708365.1_ASM2370836v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:46:34,212] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:46:34,215] [INFO] DFAST_QC result json was written to GCA_023708365.1_ASM2370836v1_genomic.fna/dqc_result.json
[2023-06-29 12:46:34,216] [INFO] DFAST_QC completed!
[2023-06-29 12:46:34,216] [INFO] Total running time: 0h0m54s