[2024-01-24 13:32:41,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,092] [INFO] DQC Reference Directory: /var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference
[2024-01-24 13:32:42,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,413] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,413] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1e73a64-4d13-4578-bf75-8640056a4688/GCF_007830125.1_ASM783012v1_genomic.fna.gz | prodigal -d GCF_007830125.1_ASM783012v1_genomic.fna/cds.fna -a GCF_007830125.1_ASM783012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:25,096] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:25,096] [INFO] Task started: HMMsearch
[2024-01-24 13:33:25,096] [INFO] Running command: hmmsearch --tblout GCF_007830125.1_ASM783012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference/reference_markers.hmm GCF_007830125.1_ASM783012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:25,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:25,492] [INFO] Found 6/6 markers.
[2024-01-24 13:33:25,551] [INFO] Query marker FASTA was written to GCF_007830125.1_ASM783012v1_genomic.fna/markers.fasta
[2024-01-24 13:33:25,551] [INFO] Task started: Blastn
[2024-01-24 13:33:25,551] [INFO] Running command: blastn -query GCF_007830125.1_ASM783012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference/reference_markers.fasta -out GCF_007830125.1_ASM783012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:26,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:26,186] [INFO] Selected 21 target genomes.
[2024-01-24 13:33:26,186] [INFO] Target genome list was writen to GCF_007830125.1_ASM783012v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:26,201] [INFO] Task started: fastANI
[2024-01-24 13:33:26,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e73a64-4d13-4578-bf75-8640056a4688/GCF_007830125.1_ASM783012v1_genomic.fna.gz --refList GCF_007830125.1_ASM783012v1_genomic.fna/target_genomes.txt --output GCF_007830125.1_ASM783012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:51,551] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:51,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:51,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:51,569] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:51,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:51,569] [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 japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	100.0	2327	2328	95	conclusive
Chitinophaga rupis	strain=DSM 21039	GCA_900109685.1	573321	573321	type	True	79.5847	1094	2328	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	79.5337	1043	2328	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	77.875	263	2328	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	77.8071	520	2328	95	below_threshold
Chitinophaga parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	77.4546	446	2328	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	77.3078	446	2328	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	77.2817	438	2328	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	77.2553	372	2328	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	77.1733	405	2328	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	77.1707	360	2328	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	77.0069	386	2328	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	76.9938	344	2328	95	below_threshold
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	76.8387	269	2328	95	below_threshold
Chitinophaga jiangningensis	strain=DSM 27406	GCA_900142605.1	1419482	1419482	type	True	76.7041	315	2328	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	75.1996	63	2328	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	75.1333	85	2328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:51,571] [INFO] DFAST Taxonomy check result was written to GCF_007830125.1_ASM783012v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:51,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:51,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:51,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference/checkm_data
[2024-01-24 13:33:51,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:51,641] [INFO] Task started: CheckM
[2024-01-24 13:33:51,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830125.1_ASM783012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830125.1_ASM783012v1_genomic.fna/checkm_input GCF_007830125.1_ASM783012v1_genomic.fna/checkm_result
[2024-01-24 13:35:33,394] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:33,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:33,416] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:33,417] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:33,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830125.1_ASM783012v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:33,418] [INFO] Task started: Blastn
[2024-01-24 13:35:33,418] [INFO] Running command: blastn -query GCF_007830125.1_ASM783012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02d3307-7270-47c9-8373-e023acf09f72/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830125.1_ASM783012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:34,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:34,228] [INFO] Selected 16 target genomes.
[2024-01-24 13:35:34,228] [INFO] Target genome list was writen to GCF_007830125.1_ASM783012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:34,304] [INFO] Task started: fastANI
[2024-01-24 13:35:34,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e73a64-4d13-4578-bf75-8640056a4688/GCF_007830125.1_ASM783012v1_genomic.fna.gz --refList GCF_007830125.1_ASM783012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830125.1_ASM783012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:54,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:54,216] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:54,216] [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_007830125.1	s__Chitinophaga japonensis	100.0	2327	2328	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_900109685.1	s__Chitinophaga rupis	79.5803	1095	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386695.1	s__Chitinophaga agrisoli	79.5281	1045	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091455.1	s__Chitinophaga sp019091455	79.4376	1071	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003568665.1	s__Chitinophaga alhagiae	77.7942	520	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003071345.1	s__Chitinophaga parva	77.4546	446	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758205.1	s__Chitinophaga sp009758205	77.273	439	2328	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	77.224	361	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994345.2	s__Chitinophaga extrema	77.2202	375	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.60	98.60	0.96	0.96	2	-
GCF_012641275.1	s__Chitinophaga varians_A	77.2112	476	2328	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	77.1733	405	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001870995.2	s__Chitinophaga sp001870995	77.1589	414	2328	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	76.989	343	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093065.1	s__Chitinophaga agri	76.8387	269	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970915.1	s__Solirubrum gummosum	75.1333	85	2328	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:54,218] [INFO] GTDB search result was written to GCF_007830125.1_ASM783012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:54,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:54,222] [INFO] DFAST_QC result json was written to GCF_007830125.1_ASM783012v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:54,223] [INFO] DFAST_QC completed!
[2024-01-24 13:35:54,223] [INFO] Total running time: 0h3m13s