[2024-01-24 13:58:10,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference
[2024-01-24 13:58:12,199] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,200] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg59994a38-5e81-4e76-9f61-0a3265b14a80/GCF_003259335.1_ASM325933v1_genomic.fna.gz | prodigal -d GCF_003259335.1_ASM325933v1_genomic.fna/cds.fna -a GCF_003259335.1_ASM325933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:42,958] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:42,958] [INFO] Task started: HMMsearch
[2024-01-24 13:58:42,958] [INFO] Running command: hmmsearch --tblout GCF_003259335.1_ASM325933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference/reference_markers.hmm GCF_003259335.1_ASM325933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:43,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:43,322] [INFO] Found 6/6 markers.
[2024-01-24 13:58:43,373] [INFO] Query marker FASTA was written to GCF_003259335.1_ASM325933v1_genomic.fna/markers.fasta
[2024-01-24 13:58:43,373] [INFO] Task started: Blastn
[2024-01-24 13:58:43,373] [INFO] Running command: blastn -query GCF_003259335.1_ASM325933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference/reference_markers.fasta -out GCF_003259335.1_ASM325933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,971] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,974] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:43,975] [INFO] Target genome list was writen to GCF_003259335.1_ASM325933v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:43,984] [INFO] Task started: fastANI
[2024-01-24 13:58:43,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg59994a38-5e81-4e76-9f61-0a3265b14a80/GCF_003259335.1_ASM325933v1_genomic.fna.gz --refList GCF_003259335.1_ASM325933v1_genomic.fna/target_genomes.txt --output GCF_003259335.1_ASM325933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:02,683] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:02,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:02,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:02,702] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:02,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:02,703] [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 skermanii	strain=DSM 23857	GCA_003259335.1	331697	331697	type	True	100.0	2022	2025	95	conclusive
Chitinophaga caeni	strain=13	GCA_002557795.1	2029983	2029983	type	True	78.2797	325	2025	95	below_threshold
Chitinophaga dinghuensis	strain=DSM 29821	GCA_003259435.1	1539050	1539050	type	True	77.4151	161	2025	95	below_threshold
Chitinophaga silvatica	strain=GDMCC 1.1288	GCA_003419895.1	2282649	2282649	type	True	77.2125	162	2025	95	below_threshold
Chitinophaga jiangningensis	strain=DSM 27406	GCA_900142605.1	1419482	1419482	type	True	77.0743	159	2025	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	77.0538	149	2025	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	77.0245	132	2025	95	below_threshold
Chitinophaga deserti	strain=XJ-2	GCA_003149455.1	2164099	2164099	type	True	76.9851	126	2025	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	76.9341	144	2025	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	76.9264	141	2025	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	76.8002	136	2025	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	76.7333	153	2025	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	76.3564	120	2025	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,704] [INFO] DFAST Taxonomy check result was written to GCF_003259335.1_ASM325933v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:02,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:02,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:02,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference/checkm_data
[2024-01-24 13:59:02,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:02,763] [INFO] Task started: CheckM
[2024-01-24 13:59:02,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259335.1_ASM325933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259335.1_ASM325933v1_genomic.fna/checkm_input GCF_003259335.1_ASM325933v1_genomic.fna/checkm_result
[2024-01-24 14:00:21,291] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:21,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:21,317] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:21,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:21,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259335.1_ASM325933v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:21,318] [INFO] Task started: Blastn
[2024-01-24 14:00:21,318] [INFO] Running command: blastn -query GCF_003259335.1_ASM325933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3054b97e-5593-4bed-a587-1b362995bf97/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259335.1_ASM325933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:22,152] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:22,157] [INFO] Selected 24 target genomes.
[2024-01-24 14:00:22,157] [INFO] Target genome list was writen to GCF_003259335.1_ASM325933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:22,229] [INFO] Task started: fastANI
[2024-01-24 14:00:22,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg59994a38-5e81-4e76-9f61-0a3265b14a80/GCF_003259335.1_ASM325933v1_genomic.fna.gz --refList GCF_003259335.1_ASM325933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259335.1_ASM325933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:52,134] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:52,150] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:52,151] [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_003259335.1	s__Chitinophaga skermanii	100.0	2022	2025	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_002557795.1	s__Chitinophaga caeni	78.2667	325	2025	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	77.4151	160	2025	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	77.397	153	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236475.1	s__Chitinophaga sp019236475	77.3493	168	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003419895.1	s__Chitinophaga sp003419895	77.2181	160	2025	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	77.0719	157	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752935.1	s__Chitinophaga sp011752935	77.0642	157	2025	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	76.9909	139	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363865.1	s__Chitinophaga sp004363865	76.9887	161	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149455.1	s__Chitinophaga deserti	76.9851	126	2025	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	76.9316	143	2025	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	76.894	122	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002290065.1	s__Chitinophaga sp002290065	76.8758	131	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168175.1	s__Chitinophaga sp902168175	76.8509	194	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927205.1	s__Chitinophaga fulva	76.8015	133	2025	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	76.6202	130	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.49	99.49	0.97	0.97	3	-
GCF_014190745.1	s__Chitinophaga sancti_A	76.5635	141	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.26	99.26	0.97	0.97	2	-
GCF_009758205.1	s__Chitinophaga sp009758205	76.386	118	2025	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	76.0518	119	2025	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 14:00:52,154] [INFO] GTDB search result was written to GCF_003259335.1_ASM325933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:52,154] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:52,158] [INFO] DFAST_QC result json was written to GCF_003259335.1_ASM325933v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:52,159] [INFO] DFAST_QC completed!
[2024-01-24 14:00:52,159] [INFO] Total running time: 0h2m41s