[2024-01-24 13:49:13,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:13,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:13,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference
[2024-01-24 13:49:15,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:15,037] [INFO] Task started: Prodigal
[2024-01-24 13:49:15,037] [INFO] Running command: gunzip -c /var/lib/cwl/stgc28c11fc-64a9-4d9c-882d-d4417e8753a1/GCF_022867795.2_ASM2286779v2_genomic.fna.gz | prodigal -d GCF_022867795.2_ASM2286779v2_genomic.fna/cds.fna -a GCF_022867795.2_ASM2286779v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:48,562] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:48,563] [INFO] Task started: HMMsearch
[2024-01-24 13:49:48,563] [INFO] Running command: hmmsearch --tblout GCF_022867795.2_ASM2286779v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference/reference_markers.hmm GCF_022867795.2_ASM2286779v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:48,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:48,871] [INFO] Found 6/6 markers.
[2024-01-24 13:49:48,919] [INFO] Query marker FASTA was written to GCF_022867795.2_ASM2286779v2_genomic.fna/markers.fasta
[2024-01-24 13:49:48,920] [INFO] Task started: Blastn
[2024-01-24 13:49:48,920] [INFO] Running command: blastn -query GCF_022867795.2_ASM2286779v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference/reference_markers.fasta -out GCF_022867795.2_ASM2286779v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:49,518] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:49,522] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:49,522] [INFO] Target genome list was writen to GCF_022867795.2_ASM2286779v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:49,543] [INFO] Task started: fastANI
[2024-01-24 13:49:49,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28c11fc-64a9-4d9c-882d-d4417e8753a1/GCF_022867795.2_ASM2286779v2_genomic.fna.gz --refList GCF_022867795.2_ASM2286779v2_genomic.fna/target_genomes.txt --output GCF_022867795.2_ASM2286779v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:17,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:17,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:17,279] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:17,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:17,280] [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 sedimenti	strain=KCTC 52590	GCA_023156195.1	2033606	2033606	type	True	81.1005	1213	2103	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	77.8317	262	2103	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	77.8237	261	2103	95	below_threshold
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	77.6497	224	2103	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	77.5731	357	2103	95	below_threshold
Chitinophaga jiangningensis	strain=DSM 27406	GCA_900142605.1	1419482	1419482	type	True	77.5221	245	2103	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	77.517	351	2103	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	77.4526	262	2103	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	77.4435	270	2103	95	below_threshold
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	77.4308	273	2103	95	below_threshold
Chitinophaga dinghuensis	strain=DSM 29821	GCA_003259435.1	1539050	1539050	type	True	77.4266	191	2103	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	77.3961	200	2103	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	77.3753	301	2103	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	77.3173	267	2103	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	77.3065	276	2103	95	below_threshold
Chitinophaga parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	77.2721	217	2103	95	below_threshold
Chitinophaga sancti	strain=DSM 784	GCA_900119105.1	1004	1004	type	True	77.2356	198	2103	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	77.2044	164	2103	95	below_threshold
Chitinophaga niabensis	strain=DSM 24787	GCA_900129465.1	536979	536979	type	True	77.1604	292	2103	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	77.0564	76	2103	95	below_threshold
Chitinophaga rupis	strain=DSM 21039	GCA_900109685.1	573321	573321	type	True	76.9448	279	2103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,281] [INFO] DFAST Taxonomy check result was written to GCF_022867795.2_ASM2286779v2_genomic.fna/tc_result.tsv
[2024-01-24 13:50:17,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:17,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:17,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference/checkm_data
[2024-01-24 13:50:17,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:17,342] [INFO] Task started: CheckM
[2024-01-24 13:50:17,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022867795.2_ASM2286779v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022867795.2_ASM2286779v2_genomic.fna/checkm_input GCF_022867795.2_ASM2286779v2_genomic.fna/checkm_result
[2024-01-24 13:51:42,844] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:42,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:42,863] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:42,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:42,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022867795.2_ASM2286779v2_genomic.fna/markers.fasta)
[2024-01-24 13:51:42,864] [INFO] Task started: Blastn
[2024-01-24 13:51:42,864] [INFO] Running command: blastn -query GCF_022867795.2_ASM2286779v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d16329d-7d78-40e6-a5de-94afa6c71ea1/dqc_reference/reference_markers_gtdb.fasta -out GCF_022867795.2_ASM2286779v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:43,637] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:43,641] [INFO] Selected 23 target genomes.
[2024-01-24 13:51:43,641] [INFO] Target genome list was writen to GCF_022867795.2_ASM2286779v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:43,694] [INFO] Task started: fastANI
[2024-01-24 13:51:43,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28c11fc-64a9-4d9c-882d-d4417e8753a1/GCF_022867795.2_ASM2286779v2_genomic.fna.gz --refList GCF_022867795.2_ASM2286779v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022867795.2_ASM2286779v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:08,994] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:09,012] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:52:09,013] [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
GCA_902168175.1	s__Chitinophaga sp902168175	80.3307	1047	2103	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	77.9817	258	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
GCF_003813775.1	s__Chitinophaga lutea	77.582	356	2103	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	77.5487	255	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142605.1	s__Chitinophaga jiangningensis	77.5277	243	2103	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	77.5217	349	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975825.1	s__Chitinophaga sp001975825	77.4593	194	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.88	98.88	0.96	0.96	2	-
GCF_012927205.1	s__Chitinophaga fulva	77.4428	261	2103	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	77.4355	268	2103	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	77.4211	190	2103	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	77.4127	274	2103	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	77.4071	296	2103	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	77.4017	338	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003412465.1	s__Chitinophaga silvisoli	77.398	199	2103	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	77.3546	310	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167325.1	s__Chitinophaga pinensis_A	77.3415	279	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.49	99.49	0.97	0.97	3	-
GCF_900167135.1	s__Chitinophaga eiseniae	77.3075	273	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003071345.1	s__Chitinophaga parva	77.2681	215	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119105.1	s__Chitinophaga sancti	77.2285	197	2103	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	77.2069	258	2103	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	77.1883	289	2103	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	77.0113	256	2103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109685.1	s__Chitinophaga rupis	76.9536	277	2103	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 13:52:09,014] [INFO] GTDB search result was written to GCF_022867795.2_ASM2286779v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:09,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:09,019] [INFO] DFAST_QC result json was written to GCF_022867795.2_ASM2286779v2_genomic.fna/dqc_result.json
[2024-01-24 13:52:09,019] [INFO] DFAST_QC completed!
[2024-01-24 13:52:09,019] [INFO] Total running time: 0h2m55s