[2023-06-28 03:04:06,548] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:04:06,550] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:04:06,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference
[2023-06-28 03:04:07,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:04:07,886] [INFO] Task started: Prodigal
[2023-06-28 03:04:07,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg82f9b491-d01d-4fcd-8b41-c7ca4acea25a/GCA_944320855.1_BRZ_FN_bin33_genomic.fna.gz | prodigal -d GCA_944320855.1_BRZ_FN_bin33_genomic.fna/cds.fna -a GCA_944320855.1_BRZ_FN_bin33_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:04:22,824] [INFO] Task succeeded: Prodigal
[2023-06-28 03:04:22,825] [INFO] Task started: HMMsearch
[2023-06-28 03:04:22,825] [INFO] Running command: hmmsearch --tblout GCA_944320855.1_BRZ_FN_bin33_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference/reference_markers.hmm GCA_944320855.1_BRZ_FN_bin33_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:04:23,074] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:04:23,077] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg82f9b491-d01d-4fcd-8b41-c7ca4acea25a/GCA_944320855.1_BRZ_FN_bin33_genomic.fna.gz]
[2023-06-28 03:04:23,106] [INFO] Query marker FASTA was written to GCA_944320855.1_BRZ_FN_bin33_genomic.fna/markers.fasta
[2023-06-28 03:04:23,106] [INFO] Task started: Blastn
[2023-06-28 03:04:23,106] [INFO] Running command: blastn -query GCA_944320855.1_BRZ_FN_bin33_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference/reference_markers.fasta -out GCA_944320855.1_BRZ_FN_bin33_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:04:23,722] [INFO] Task succeeded: Blastn
[2023-06-28 03:04:23,726] [INFO] Selected 16 target genomes.
[2023-06-28 03:04:23,727] [INFO] Target genome list was writen to GCA_944320855.1_BRZ_FN_bin33_genomic.fna/target_genomes.txt
[2023-06-28 03:04:23,728] [INFO] Task started: fastANI
[2023-06-28 03:04:23,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f9b491-d01d-4fcd-8b41-c7ca4acea25a/GCA_944320855.1_BRZ_FN_bin33_genomic.fna.gz --refList GCA_944320855.1_BRZ_FN_bin33_genomic.fna/target_genomes.txt --output GCA_944320855.1_BRZ_FN_bin33_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:04:34,325] [INFO] Task succeeded: fastANI
[2023-06-28 03:04:34,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:04:34,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:04:34,337] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:04:34,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:04:34,337] [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
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.2605	203	1051	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.1073	207	1051	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	78.7993	197	1051	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.3614	210	1051	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.152	224	1051	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.128	97	1051	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	77.0091	112	1051	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	76.9017	114	1051	95	below_threshold
Bacteroides luti	strain=DSM 26991	GCA_900128905.1	1297750	1297750	type	True	76.9012	61	1051	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	76.8675	91	1051	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	76.7722	116	1051	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	76.6627	93	1051	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	76.6544	94	1051	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:04:34,339] [INFO] DFAST Taxonomy check result was written to GCA_944320855.1_BRZ_FN_bin33_genomic.fna/tc_result.tsv
[2023-06-28 03:04:34,340] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:04:34,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:04:34,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference/checkm_data
[2023-06-28 03:04:34,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:04:34,380] [INFO] Task started: CheckM
[2023-06-28 03:04:34,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320855.1_BRZ_FN_bin33_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320855.1_BRZ_FN_bin33_genomic.fna/checkm_input GCA_944320855.1_BRZ_FN_bin33_genomic.fna/checkm_result
[2023-06-28 03:05:20,185] [INFO] Task succeeded: CheckM
[2023-06-28 03:05:20,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:05:20,210] [INFO] ===== Completeness check finished =====
[2023-06-28 03:05:20,210] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:05:20,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320855.1_BRZ_FN_bin33_genomic.fna/markers.fasta)
[2023-06-28 03:05:20,211] [INFO] Task started: Blastn
[2023-06-28 03:05:20,211] [INFO] Running command: blastn -query GCA_944320855.1_BRZ_FN_bin33_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5729e4-f0c2-460a-9c0f-de4ac3ba19f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320855.1_BRZ_FN_bin33_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:05:21,021] [INFO] Task succeeded: Blastn
[2023-06-28 03:05:21,026] [INFO] Selected 8 target genomes.
[2023-06-28 03:05:21,026] [INFO] Target genome list was writen to GCA_944320855.1_BRZ_FN_bin33_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:05:21,031] [INFO] Task started: fastANI
[2023-06-28 03:05:21,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f9b491-d01d-4fcd-8b41-c7ca4acea25a/GCA_944320855.1_BRZ_FN_bin33_genomic.fna.gz --refList GCA_944320855.1_BRZ_FN_bin33_genomic.fna/target_genomes_gtdb.txt --output GCA_944320855.1_BRZ_FN_bin33_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:05:26,571] [INFO] Task succeeded: fastANI
[2023-06-28 03:05:26,582] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:05:26,582] [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_900544075.1	s__Phocaeicola sp900544075	93.8043	690	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018884025.1	s__Phocaeicola faecipullorum_A	86.5418	576	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.13	97.13	0.68	0.68	2	-
GCA_018883555.1	s__Phocaeicola faecigallinarum	86.1663	565	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901995.1	s__Phocaeicola sp900066445	85.8997	619	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.12	97.12	0.79	0.79	3	-
GCF_016902295.1	s__Phocaeicola caecigallinarum_A	84.8646	561	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.48	97.48	0.83	0.83	2	-
GCF_000187895.1	s__Phocaeicola plebeius	78.1715	221	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_900553185.1	s__Phocaeicola sp900553185	78.1005	136	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCA_000436795.1	s__Phocaeicola sp000436795	77.7003	153	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-28 03:05:26,584] [INFO] GTDB search result was written to GCA_944320855.1_BRZ_FN_bin33_genomic.fna/result_gtdb.tsv
[2023-06-28 03:05:26,585] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:05:26,588] [INFO] DFAST_QC result json was written to GCA_944320855.1_BRZ_FN_bin33_genomic.fna/dqc_result.json
[2023-06-28 03:05:26,588] [INFO] DFAST_QC completed!
[2023-06-28 03:05:26,589] [INFO] Total running time: 0h1m20s