[2024-01-24 11:26:38,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference
[2024-01-24 11:26:40,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,151] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a52f1ca-06c0-480a-99a6-9c5404f48eb5/GCF_003071345.1_ASM307134v1_genomic.fna.gz | prodigal -d GCF_003071345.1_ASM307134v1_genomic.fna/cds.fna -a GCF_003071345.1_ASM307134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:18,063] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:18,064] [INFO] Task started: HMMsearch
[2024-01-24 11:27:18,064] [INFO] Running command: hmmsearch --tblout GCF_003071345.1_ASM307134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference/reference_markers.hmm GCF_003071345.1_ASM307134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:18,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:18,390] [INFO] Found 6/6 markers.
[2024-01-24 11:27:18,442] [INFO] Query marker FASTA was written to GCF_003071345.1_ASM307134v1_genomic.fna/markers.fasta
[2024-01-24 11:27:18,442] [INFO] Task started: Blastn
[2024-01-24 11:27:18,443] [INFO] Running command: blastn -query GCF_003071345.1_ASM307134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference/reference_markers.fasta -out GCF_003071345.1_ASM307134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:19,042] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:19,045] [INFO] Selected 22 target genomes.
[2024-01-24 11:27:19,045] [INFO] Target genome list was writen to GCF_003071345.1_ASM307134v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:19,069] [INFO] Task started: fastANI
[2024-01-24 11:27:19,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a52f1ca-06c0-480a-99a6-9c5404f48eb5/GCF_003071345.1_ASM307134v1_genomic.fna.gz --refList GCF_003071345.1_ASM307134v1_genomic.fna/target_genomes.txt --output GCF_003071345.1_ASM307134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:39,528] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:39,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:39,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:39,550] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:39,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:39,551] [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 parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	100.0	2044	2044	95	conclusive
Chitinophaga costaii	strain=A37T2	GCA_003071385.1	1335309	1335309	type	True	79.8397	813	2044	95	below_threshold
Chitinophaga costaii	strain=A37T2	GCA_900094705.1	1335309	1335309	type	True	79.8001	822	2044	95	below_threshold
Chitinophaga japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	77.5387	423	2044	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	77.4881	202	2044	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	77.4084	297	2044	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	77.3178	345	2044	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	77.2861	362	2044	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	77.2656	361	2044	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	77.19	308	2044	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	77.1382	204	2044	95	below_threshold
Chitinophaga jiangningensis	strain=DSM 27406	GCA_900142605.1	1419482	1419482	type	True	76.8137	257	2044	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:39,553] [INFO] DFAST Taxonomy check result was written to GCF_003071345.1_ASM307134v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:39,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:39,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:39,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference/checkm_data
[2024-01-24 11:27:39,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:39,615] [INFO] Task started: CheckM
[2024-01-24 11:27:39,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003071345.1_ASM307134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003071345.1_ASM307134v1_genomic.fna/checkm_input GCF_003071345.1_ASM307134v1_genomic.fna/checkm_result
[2024-01-24 11:29:15,949] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:15,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:15,975] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:15,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:15,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003071345.1_ASM307134v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:15,976] [INFO] Task started: Blastn
[2024-01-24 11:29:15,976] [INFO] Running command: blastn -query GCF_003071345.1_ASM307134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71507993-4479-4ad7-810e-dcc235b627ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_003071345.1_ASM307134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:16,800] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:16,805] [INFO] Selected 22 target genomes.
[2024-01-24 11:29:16,805] [INFO] Target genome list was writen to GCF_003071345.1_ASM307134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:16,844] [INFO] Task started: fastANI
[2024-01-24 11:29:16,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a52f1ca-06c0-480a-99a6-9c5404f48eb5/GCF_003071345.1_ASM307134v1_genomic.fna.gz --refList GCF_003071345.1_ASM307134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003071345.1_ASM307134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:41,146] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:41,168] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:41,168] [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_003071345.1	s__Chitinophaga parva	100.0	2044	2044	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_900094705.1	s__Chitinophaga costaii	79.8061	821	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007830125.1	s__Chitinophaga japonensis	77.5456	422	2044	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	77.5066	362	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003807585.1	s__Chitinophaga barathri	77.4894	311	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003813775.1	s__Chitinophaga lutea	77.422	294	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516355.1	s__Chitinophaga sp012516355	77.4175	340	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
GCF_019091455.1	s__Chitinophaga sp019091455	77.3647	375	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742215.1	s__Chitinophaga sp017742215	77.322	312	2044	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	77.2788	362	2044	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	77.2739	359	2044	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	77.2705	282	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529935.1	s__Chitinophaga qingshengii	77.2246	303	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849435.1	s__Chitinophaga niabensis_A	77.1863	249	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412465.1	s__Chitinophaga silvisoli	77.1655	203	2044	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	77.155	265	2044	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467415.1	s__Chitinophaga sp016467415	76.9258	256	2044	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	76.6582	263	2044	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 11:29:41,169] [INFO] GTDB search result was written to GCF_003071345.1_ASM307134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:41,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:41,174] [INFO] DFAST_QC result json was written to GCF_003071345.1_ASM307134v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:41,174] [INFO] DFAST_QC completed!
[2024-01-24 11:29:41,174] [INFO] Total running time: 0h3m2s