[2024-01-24 12:42:06,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:06,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:06,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference
[2024-01-24 12:42:07,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:07,683] [INFO] Task started: Prodigal
[2024-01-24 12:42:07,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b20891-7ab0-4f77-9bce-e00cdad7ae67/GCF_009758125.1_ASM975812v1_genomic.fna.gz | prodigal -d GCF_009758125.1_ASM975812v1_genomic.fna/cds.fna -a GCF_009758125.1_ASM975812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:43,133] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:43,134] [INFO] Task started: HMMsearch
[2024-01-24 12:42:43,134] [INFO] Running command: hmmsearch --tblout GCF_009758125.1_ASM975812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference/reference_markers.hmm GCF_009758125.1_ASM975812v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:43,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:43,515] [INFO] Found 6/6 markers.
[2024-01-24 12:42:43,585] [INFO] Query marker FASTA was written to GCF_009758125.1_ASM975812v1_genomic.fna/markers.fasta
[2024-01-24 12:42:43,585] [INFO] Task started: Blastn
[2024-01-24 12:42:43,586] [INFO] Running command: blastn -query GCF_009758125.1_ASM975812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference/reference_markers.fasta -out GCF_009758125.1_ASM975812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:44,188] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:44,192] [INFO] Selected 15 target genomes.
[2024-01-24 12:42:44,193] [INFO] Target genome list was writen to GCF_009758125.1_ASM975812v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:44,199] [INFO] Task started: fastANI
[2024-01-24 12:42:44,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b20891-7ab0-4f77-9bce-e00cdad7ae67/GCF_009758125.1_ASM975812v1_genomic.fna.gz --refList GCF_009758125.1_ASM975812v1_genomic.fna/target_genomes.txt --output GCF_009758125.1_ASM975812v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:43:03,381] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:03,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:43:03,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:43:03,394] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:43:03,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:43:03,395] [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 oryziterrae	strain=JCM 16595	GCA_009758125.1	1031224	1031224	type	True	100.0	2681	2684	95	conclusive
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	78.9536	791	2684	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	78.898	743	2684	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	78.7291	794	2684	95	below_threshold
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	78.6199	706	2684	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	78.5767	602	2684	95	below_threshold
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	78.4995	624	2684	95	below_threshold
Chitinophaga sancti	strain=DSM 784	GCA_900119105.1	1004	1004	type	True	78.3313	614	2684	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	77.5208	310	2684	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	77.4874	344	2684	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	75.7671	88	2684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:43:03,397] [INFO] DFAST Taxonomy check result was written to GCF_009758125.1_ASM975812v1_genomic.fna/tc_result.tsv
[2024-01-24 12:43:03,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:43:03,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:43:03,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference/checkm_data
[2024-01-24 12:43:03,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:43:03,472] [INFO] Task started: CheckM
[2024-01-24 12:43:03,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009758125.1_ASM975812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009758125.1_ASM975812v1_genomic.fna/checkm_input GCF_009758125.1_ASM975812v1_genomic.fna/checkm_result
[2024-01-24 12:44:38,546] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:38,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:38,573] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:38,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:38,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009758125.1_ASM975812v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:38,574] [INFO] Task started: Blastn
[2024-01-24 12:44:38,574] [INFO] Running command: blastn -query GCF_009758125.1_ASM975812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37ea6e76-f0ad-49ed-8810-8da34761b229/dqc_reference/reference_markers_gtdb.fasta -out GCF_009758125.1_ASM975812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:39,389] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:39,394] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:39,395] [INFO] Target genome list was writen to GCF_009758125.1_ASM975812v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:39,497] [INFO] Task started: fastANI
[2024-01-24 12:44:39,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b20891-7ab0-4f77-9bce-e00cdad7ae67/GCF_009758125.1_ASM975812v1_genomic.fna.gz --refList GCF_009758125.1_ASM975812v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009758125.1_ASM975812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:59,668] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:59,678] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:59,679] [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_009758125.1	s__Chitinophaga oryziterrae	100.0	2681	2684	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_900110995.1	s__Chitinophaga sp900110995	90.9674	2035	2684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112615.1	s__Chitinophaga sp900112615	82.3684	1499	2684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142925.1	s__Chitinophaga sp900142925	79.1325	759	2684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014595.1	s__Chitinophaga ginsengisoli	78.94	793	2684	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	78.8924	743	2684	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	78.8443	657	2684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.88	98.88	0.96	0.96	2	-
GCF_003182155.1	s__Chitinophaga sp003182155	78.763	714	2684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102545.1	s__Chitinophaga filiformis	78.7313	793	2684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168105.1	s__Chitinophaga sp902168105	78.6043	695	2684	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	78.3313	614	2684	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	77.5814	447	2684	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	77.5242	309	2684	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 12:44:59,680] [INFO] GTDB search result was written to GCF_009758125.1_ASM975812v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:59,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:59,684] [INFO] DFAST_QC result json was written to GCF_009758125.1_ASM975812v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:59,684] [INFO] DFAST_QC completed!
[2024-01-24 12:44:59,685] [INFO] Total running time: 0h2m53s