[2024-01-24 14:37:45,831] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:45,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:45,836] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference
[2024-01-24 14:37:49,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:49,294] [INFO] Task started: Prodigal
[2024-01-24 14:37:49,295] [INFO] Running command: gunzip -c /var/lib/cwl/stgafaa24ad-4af0-4223-a3df-8744e1d25037/GCF_002557795.1_ASM255779v1_genomic.fna.gz | prodigal -d GCF_002557795.1_ASM255779v1_genomic.fna/cds.fna -a GCF_002557795.1_ASM255779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:15,828] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:15,828] [INFO] Task started: HMMsearch
[2024-01-24 14:38:15,829] [INFO] Running command: hmmsearch --tblout GCF_002557795.1_ASM255779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference/reference_markers.hmm GCF_002557795.1_ASM255779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:16,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:16,171] [INFO] Found 6/6 markers.
[2024-01-24 14:38:16,216] [INFO] Query marker FASTA was written to GCF_002557795.1_ASM255779v1_genomic.fna/markers.fasta
[2024-01-24 14:38:16,216] [INFO] Task started: Blastn
[2024-01-24 14:38:16,216] [INFO] Running command: blastn -query GCF_002557795.1_ASM255779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference/reference_markers.fasta -out GCF_002557795.1_ASM255779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:16,849] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:16,854] [INFO] Selected 21 target genomes.
[2024-01-24 14:38:16,855] [INFO] Target genome list was writen to GCF_002557795.1_ASM255779v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:16,903] [INFO] Task started: fastANI
[2024-01-24 14:38:16,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgafaa24ad-4af0-4223-a3df-8744e1d25037/GCF_002557795.1_ASM255779v1_genomic.fna.gz --refList GCF_002557795.1_ASM255779v1_genomic.fna/target_genomes.txt --output GCF_002557795.1_ASM255779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:42,387] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:42,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:42,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:42,402] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:42,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:42,403] [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 caeni	strain=13	GCA_002557795.1	2029983	2029983	type	True	100.0	1759	1759	95	conclusive
Chitinophaga skermanii	strain=DSM 23857	GCA_003259335.1	331697	331697	type	True	78.4391	318	1759	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	77.9043	124	1759	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	77.7128	118	1759	95	below_threshold
Chitinophaga silvatica	strain=GDMCC 1.1288	GCA_003419895.1	2282649	2282649	type	True	77.3906	118	1759	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	77.3206	111	1759	95	below_threshold
Chitinophaga terrae (ex Kim and Jung 2007)	strain=DSM 23920	GCA_900107795.1	408074	408074	type	True	77.2266	153	1759	95	below_threshold
Chitinophaga niabensis	strain=DSM 24787	GCA_900129465.1	536979	536979	type	True	77.1983	132	1759	95	below_threshold
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	77.1416	120	1759	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	77.131	129	1759	95	below_threshold
Chitinophaga jiangningensis	strain=DSM 27406	GCA_900142605.1	1419482	1419482	type	True	76.9872	134	1759	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	76.9295	139	1759	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	76.9291	75	1759	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	76.9153	136	1759	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	76.9065	116	1759	95	below_threshold
Chitinophaga deserti	strain=XJ-2	GCA_003149455.1	2164099	2164099	type	True	76.7482	135	1759	95	below_threshold
Chitinophaga sancti	strain=DSM 784	GCA_900119105.1	1004	1004	type	True	76.6564	104	1759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:42,404] [INFO] DFAST Taxonomy check result was written to GCF_002557795.1_ASM255779v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:42,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:42,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:42,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference/checkm_data
[2024-01-24 14:38:42,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:42,463] [INFO] Task started: CheckM
[2024-01-24 14:38:42,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002557795.1_ASM255779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002557795.1_ASM255779v1_genomic.fna/checkm_input GCF_002557795.1_ASM255779v1_genomic.fna/checkm_result
[2024-01-24 14:39:51,474] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:51,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:51,504] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:51,505] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:51,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002557795.1_ASM255779v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:51,507] [INFO] Task started: Blastn
[2024-01-24 14:39:51,507] [INFO] Running command: blastn -query GCF_002557795.1_ASM255779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9befc3e-467f-40df-a7aa-28761659a15d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002557795.1_ASM255779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:52,432] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:52,437] [INFO] Selected 21 target genomes.
[2024-01-24 14:39:52,437] [INFO] Target genome list was writen to GCF_002557795.1_ASM255779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:52,482] [INFO] Task started: fastANI
[2024-01-24 14:39:52,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgafaa24ad-4af0-4223-a3df-8744e1d25037/GCF_002557795.1_ASM255779v1_genomic.fna.gz --refList GCF_002557795.1_ASM255779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002557795.1_ASM255779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:20,689] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:20,708] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:20,709] [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_002557795.1	s__Chitinophaga caeni	100.0	1759	1759	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_003259335.1	s__Chitinophaga skermanii	78.4474	318	1759	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	77.8294	122	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
GCF_902167325.1	s__Chitinophaga pinensis_A	77.7365	114	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.49	99.49	0.97	0.97	3	-
GCA_001870995.2	s__Chitinophaga sp001870995	77.6052	132	1759	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	77.5308	149	1759	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	77.4203	116	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829335.1	s__Chitinophaga polysaccharea_B	77.3365	125	1759	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	77.3257	110	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107795.1	s__Chitinophaga terrae	77.2495	153	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009647655.1	s__Chitinophaga sp009647655	77.2285	134	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019219075.1	s__Chitinophaga sp019219075	77.2094	135	1759	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	77.1879	131	1759	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	77.131	129	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014755.1	s__Chitinophaga niastensis	76.9635	120	1759	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	76.9472	138	1759	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	76.9308	135	1759	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	76.9041	115	1759	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	76.7221	107	1759	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	76.6551	103	1759	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 14:40:20,711] [INFO] GTDB search result was written to GCF_002557795.1_ASM255779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:20,712] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:20,717] [INFO] DFAST_QC result json was written to GCF_002557795.1_ASM255779v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:20,717] [INFO] DFAST_QC completed!
[2024-01-24 14:40:20,717] [INFO] Total running time: 0h2m35s