[2024-01-25 18:48:35,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,682] [INFO] DQC Reference Directory: /var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference
[2024-01-25 18:48:36,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,865] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,865] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2595bdb-a7c0-46f1-8390-ade283e9f764/GCF_003813775.1_ASM381377v1_genomic.fna.gz | prodigal -d GCF_003813775.1_ASM381377v1_genomic.fna/cds.fna -a GCF_003813775.1_ASM381377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:13,006] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:13,006] [INFO] Task started: HMMsearch
[2024-01-25 18:49:13,006] [INFO] Running command: hmmsearch --tblout GCF_003813775.1_ASM381377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference/reference_markers.hmm GCF_003813775.1_ASM381377v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:13,300] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:13,301] [INFO] Found 6/6 markers.
[2024-01-25 18:49:13,350] [INFO] Query marker FASTA was written to GCF_003813775.1_ASM381377v1_genomic.fna/markers.fasta
[2024-01-25 18:49:13,351] [INFO] Task started: Blastn
[2024-01-25 18:49:13,351] [INFO] Running command: blastn -query GCF_003813775.1_ASM381377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference/reference_markers.fasta -out GCF_003813775.1_ASM381377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:13,903] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:13,906] [INFO] Selected 21 target genomes.
[2024-01-25 18:49:13,906] [INFO] Target genome list was writen to GCF_003813775.1_ASM381377v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:13,917] [INFO] Task started: fastANI
[2024-01-25 18:49:13,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2595bdb-a7c0-46f1-8390-ade283e9f764/GCF_003813775.1_ASM381377v1_genomic.fna.gz --refList GCF_003813775.1_ASM381377v1_genomic.fna/target_genomes.txt --output GCF_003813775.1_ASM381377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:34,433] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:34,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:34,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:34,442] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:34,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:34,442] [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 lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	100.0	2201	2201	95	conclusive
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	82.8142	594	2201	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	82.2548	1247	2201	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	80.511	1004	2201	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	80.0487	950	2201	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003614855.1	1647451	1647451	type	True	80.0056	956	2201	95	below_threshold
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	79.3475	808	2201	95	below_threshold
Chitinophaga niabensis	strain=DSM 24787	GCA_900129465.1	536979	536979	type	True	78.6637	640	2201	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	77.3618	221	2201	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	77.0363	262	2201	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.7792	58	2201	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	75.1717	59	2201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:34,443] [INFO] DFAST Taxonomy check result was written to GCF_003813775.1_ASM381377v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:34,444] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:34,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:34,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference/checkm_data
[2024-01-25 18:49:34,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:34,516] [INFO] Task started: CheckM
[2024-01-25 18:49:34,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003813775.1_ASM381377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003813775.1_ASM381377v1_genomic.fna/checkm_input GCF_003813775.1_ASM381377v1_genomic.fna/checkm_result
[2024-01-25 18:51:06,087] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:06,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:06,110] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:06,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:06,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003813775.1_ASM381377v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:06,111] [INFO] Task started: Blastn
[2024-01-25 18:51:06,111] [INFO] Running command: blastn -query GCF_003813775.1_ASM381377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef427682-690a-4991-8ce8-68ee8ce003a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003813775.1_ASM381377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:07,015] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:07,019] [INFO] Selected 16 target genomes.
[2024-01-25 18:51:07,019] [INFO] Target genome list was writen to GCF_003813775.1_ASM381377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:07,042] [INFO] Task started: fastANI
[2024-01-25 18:51:07,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2595bdb-a7c0-46f1-8390-ade283e9f764/GCF_003813775.1_ASM381377v1_genomic.fna.gz --refList GCF_003813775.1_ASM381377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003813775.1_ASM381377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:24,614] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:24,623] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:24,624] [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_003813775.1	s__Chitinophaga lutea	100.0	2201	2201	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_003568665.1	s__Chitinophaga alhagiae	82.2548	1247	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017742215.1	s__Chitinophaga sp017742215	80.5109	1004	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003807585.1	s__Chitinophaga barathri	80.0561	948	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007992715.1	s__Chitinophaga cymbidii	79.933	870	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086345.1	s__Chitinophaga sp008086345	79.397	728	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958645.1	s__Chitinophaga rhizosphaerae	79.3533	807	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129465.1	s__Chitinophaga niabensis	78.6575	641	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094705.1	s__Chitinophaga costaii	77.1776	184	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003944715.1	s__Hymenobacter rigui	75.1717	59	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	75.1676	63	2201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:24,625] [INFO] GTDB search result was written to GCF_003813775.1_ASM381377v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:24,626] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:24,628] [INFO] DFAST_QC result json was written to GCF_003813775.1_ASM381377v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:24,629] [INFO] DFAST_QC completed!
[2024-01-25 18:51:24,629] [INFO] Total running time: 0h2m49s