[2024-01-24 12:21:57,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,555] [INFO] DQC Reference Directory: /var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference
[2024-01-24 12:21:58,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,744] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg535363bb-bbd5-4feb-848a-54ed52a985a8/GCF_902167635.1_PRJEB33168_genomic.fna.gz | prodigal -d GCF_902167635.1_PRJEB33168_genomic.fna/cds.fna -a GCF_902167635.1_PRJEB33168_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:34,397] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:34,397] [INFO] Task started: HMMsearch
[2024-01-24 12:22:34,397] [INFO] Running command: hmmsearch --tblout GCF_902167635.1_PRJEB33168_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference/reference_markers.hmm GCF_902167635.1_PRJEB33168_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:34,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:34,715] [INFO] Found 6/6 markers.
[2024-01-24 12:22:34,765] [INFO] Query marker FASTA was written to GCF_902167635.1_PRJEB33168_genomic.fna/markers.fasta
[2024-01-24 12:22:34,766] [INFO] Task started: Blastn
[2024-01-24 12:22:34,766] [INFO] Running command: blastn -query GCF_902167635.1_PRJEB33168_genomic.fna/markers.fasta -db /var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference/reference_markers.fasta -out GCF_902167635.1_PRJEB33168_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:35,353] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:35,357] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:35,357] [INFO] Target genome list was writen to GCF_902167635.1_PRJEB33168_genomic.fna/target_genomes.txt
[2024-01-24 12:22:35,363] [INFO] Task started: fastANI
[2024-01-24 12:22:35,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg535363bb-bbd5-4feb-848a-54ed52a985a8/GCF_902167635.1_PRJEB33168_genomic.fna.gz --refList GCF_902167635.1_PRJEB33168_genomic.fna/target_genomes.txt --output GCF_902167635.1_PRJEB33168_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:00,589] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:00,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:00,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:00,602] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:00,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:00,602] [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
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	100.0	2079	2096	95	conclusive
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	79.6036	868	2096	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	79.5414	820	2096	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	79.5236	832	2096	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	79.5232	822	2096	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	79.4097	779	2096	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	79.4071	821	2096	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	79.4069	823	2096	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	79.3108	741	2096	95	below_threshold
Chitinophaga dinghuensis	strain=DSM 29821	GCA_003259435.1	1539050	1539050	type	True	79.2995	649	2096	95	below_threshold
Chitinophaga niastensis	strain=DSM 24859	GCA_003014755.1	536980	536980	type	True	79.2058	773	2096	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	79.087	746	2096	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	77.5953	253	2096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:00,605] [INFO] DFAST Taxonomy check result was written to GCF_902167635.1_PRJEB33168_genomic.fna/tc_result.tsv
[2024-01-24 12:23:00,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:00,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:00,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference/checkm_data
[2024-01-24 12:23:00,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:00,666] [INFO] Task started: CheckM
[2024-01-24 12:23:00,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902167635.1_PRJEB33168_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902167635.1_PRJEB33168_genomic.fna/checkm_input GCF_902167635.1_PRJEB33168_genomic.fna/checkm_result
[2024-01-24 12:24:35,000] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:35,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:35,021] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:35,022] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:35,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902167635.1_PRJEB33168_genomic.fna/markers.fasta)
[2024-01-24 12:24:35,022] [INFO] Task started: Blastn
[2024-01-24 12:24:35,022] [INFO] Running command: blastn -query GCF_902167635.1_PRJEB33168_genomic.fna/markers.fasta -db /var/lib/cwl/stga23b9a0f-122b-411c-87e3-eb545d85bf1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_902167635.1_PRJEB33168_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:35,777] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:35,780] [INFO] Selected 17 target genomes.
[2024-01-24 12:24:35,780] [INFO] Target genome list was writen to GCF_902167635.1_PRJEB33168_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:35,821] [INFO] Task started: fastANI
[2024-01-24 12:24:35,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg535363bb-bbd5-4feb-848a-54ed52a985a8/GCF_902167635.1_PRJEB33168_genomic.fna.gz --refList GCF_902167635.1_PRJEB33168_genomic.fna/target_genomes_gtdb.txt --output GCF_902167635.1_PRJEB33168_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:59,485] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:59,499] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:59,499] [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_902167635.1	s__Chitinophaga vietnamensis	100.0	2081	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_012516355.1	s__Chitinophaga sp012516355	79.6326	856	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
GCF_003994345.2	s__Chitinophaga extrema	79.5651	824	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.60	98.60	0.96	0.96	2	-
GCA_001870995.2	s__Chitinophaga sp001870995	79.5389	744	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167135.1	s__Chitinophaga eiseniae	79.5379	820	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529945.1	s__Chitinophaga varians	79.5138	823	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018255755.1	s__Chitinophaga sp018255755	79.476	796	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641275.1	s__Chitinophaga varians_A	79.4387	829	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003308995.1	s__Chitinophaga flava	79.4098	779	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927205.1	s__Chitinophaga fulva	79.4034	822	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110835.1	s__Chitinophaga arvensicola	79.32	739	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259435.1	s__Chitinophaga dinghuensis	79.3062	647	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236475.1	s__Chitinophaga sp019236475	79.2191	617	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014755.1	s__Chitinophaga niastensis	79.2058	773	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641265.1	s__Chitinophaga eiseniae_A	79.1572	763	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829335.1	s__Chitinophaga polysaccharea_B	79.113	746	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726295.1	s__Chitinophaga sp012726295	79.0612	731	2096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.43	99.43	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:59,501] [INFO] GTDB search result was written to GCF_902167635.1_PRJEB33168_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:59,502] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:59,506] [INFO] DFAST_QC result json was written to GCF_902167635.1_PRJEB33168_genomic.fna/dqc_result.json
[2024-01-24 12:24:59,506] [INFO] DFAST_QC completed!
[2024-01-24 12:24:59,506] [INFO] Total running time: 0h3m2s