[2024-01-24 13:09:51,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference
[2024-01-24 13:09:53,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,146] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d9cef4a-f8b5-4bc8-9148-99b9e35972e8/GCF_003014755.1_ASM301475v1_genomic.fna.gz | prodigal -d GCF_003014755.1_ASM301475v1_genomic.fna/cds.fna -a GCF_003014755.1_ASM301475v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:26,710] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:26,711] [INFO] Task started: HMMsearch
[2024-01-24 13:10:26,711] [INFO] Running command: hmmsearch --tblout GCF_003014755.1_ASM301475v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference/reference_markers.hmm GCF_003014755.1_ASM301475v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:27,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:27,115] [INFO] Found 6/6 markers.
[2024-01-24 13:10:27,174] [INFO] Query marker FASTA was written to GCF_003014755.1_ASM301475v1_genomic.fna/markers.fasta
[2024-01-24 13:10:27,175] [INFO] Task started: Blastn
[2024-01-24 13:10:27,175] [INFO] Running command: blastn -query GCF_003014755.1_ASM301475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference/reference_markers.fasta -out GCF_003014755.1_ASM301475v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:27,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:27,824] [INFO] Selected 11 target genomes.
[2024-01-24 13:10:27,824] [INFO] Target genome list was writen to GCF_003014755.1_ASM301475v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:27,830] [INFO] Task started: fastANI
[2024-01-24 13:10:27,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d9cef4a-f8b5-4bc8-9148-99b9e35972e8/GCF_003014755.1_ASM301475v1_genomic.fna.gz --refList GCF_003014755.1_ASM301475v1_genomic.fna/target_genomes.txt --output GCF_003014755.1_ASM301475v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:44,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:44,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:44,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:44,266] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:44,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:44,266] [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 niastensis	strain=DSM 24859	GCA_003014755.1	536980	536980	type	True	100.0	2423	2424	95	conclusive
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	81.4484	1110	2424	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	81.3433	1067	2424	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	81.2764	1142	2424	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	79.6348	819	2424	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	79.3749	834	2424	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	79.2389	746	2424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:44,267] [INFO] DFAST Taxonomy check result was written to GCF_003014755.1_ASM301475v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:44,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:44,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:44,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference/checkm_data
[2024-01-24 13:10:44,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:44,344] [INFO] Task started: CheckM
[2024-01-24 13:10:44,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014755.1_ASM301475v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014755.1_ASM301475v1_genomic.fna/checkm_input GCF_003014755.1_ASM301475v1_genomic.fna/checkm_result
[2024-01-24 13:12:13,156] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:13,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:13,180] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:13,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:13,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014755.1_ASM301475v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:13,182] [INFO] Task started: Blastn
[2024-01-24 13:12:13,182] [INFO] Running command: blastn -query GCF_003014755.1_ASM301475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bbf0601-e2b7-42db-bb1e-8d5e52b62ee5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014755.1_ASM301475v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:13,988] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:13,992] [INFO] Selected 8 target genomes.
[2024-01-24 13:12:13,992] [INFO] Target genome list was writen to GCF_003014755.1_ASM301475v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:14,006] [INFO] Task started: fastANI
[2024-01-24 13:12:14,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d9cef4a-f8b5-4bc8-9148-99b9e35972e8/GCF_003014755.1_ASM301475v1_genomic.fna.gz --refList GCF_003014755.1_ASM301475v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014755.1_ASM301475v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:28,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:28,674] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:28,674] [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_003014755.1	s__Chitinophaga niastensis	100.0	2423	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004363865.1	s__Chitinophaga sp004363865	81.7223	1283	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168065.1	s__Chitinophaga ginsengisegetis	81.4494	1111	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.27	98.27	0.94	0.94	3	-
GCF_900110835.1	s__Chitinophaga arvensicola	81.3351	1069	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224885.1	s__Chitinophaga sp018224885	81.2721	1143	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745275.1	s__Chitinophaga sp017745275	80.8189	1084	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150045.1	s__Chitinophaga polysaccharea_A	80.7366	1026	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	96.96	96.96	0.91	0.91	2	-
GCF_007829335.1	s__Chitinophaga polysaccharea_B	80.6092	973	2424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:28,676] [INFO] GTDB search result was written to GCF_003014755.1_ASM301475v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:28,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:28,681] [INFO] DFAST_QC result json was written to GCF_003014755.1_ASM301475v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:28,681] [INFO] DFAST_QC completed!
[2024-01-24 13:12:28,682] [INFO] Total running time: 0h2m37s