[2024-01-24 12:47:09,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:09,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:09,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference
[2024-01-24 12:47:11,109] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:11,110] [INFO] Task started: Prodigal
[2024-01-24 12:47:11,110] [INFO] Running command: gunzip -c /var/lib/cwl/stgc783ea28-75cc-400f-b2e7-65dd796782ce/GCF_000024005.1_ASM2400v1_genomic.fna.gz | prodigal -d GCF_000024005.1_ASM2400v1_genomic.fna/cds.fna -a GCF_000024005.1_ASM2400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:05,027] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:05,028] [INFO] Task started: HMMsearch
[2024-01-24 12:48:05,028] [INFO] Running command: hmmsearch --tblout GCF_000024005.1_ASM2400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference/reference_markers.hmm GCF_000024005.1_ASM2400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:05,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:05,454] [INFO] Found 6/6 markers.
[2024-01-24 12:48:05,521] [INFO] Query marker FASTA was written to GCF_000024005.1_ASM2400v1_genomic.fna/markers.fasta
[2024-01-24 12:48:05,522] [INFO] Task started: Blastn
[2024-01-24 12:48:05,522] [INFO] Running command: blastn -query GCF_000024005.1_ASM2400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference/reference_markers.fasta -out GCF_000024005.1_ASM2400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:06,131] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:06,135] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:06,136] [INFO] Target genome list was writen to GCF_000024005.1_ASM2400v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:06,142] [INFO] Task started: fastANI
[2024-01-24 12:48:06,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgc783ea28-75cc-400f-b2e7-65dd796782ce/GCF_000024005.1_ASM2400v1_genomic.fna.gz --refList GCF_000024005.1_ASM2400v1_genomic.fna/target_genomes.txt --output GCF_000024005.1_ASM2400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:22,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:22,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:22,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:22,232] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:22,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:22,232] [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 pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	100.0	3041	3042	95	conclusive
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	82.5948	1665	3042	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	81.987	1475	3042	95	below_threshold
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	81.1769	1351	3042	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	81.1713	1415	3042	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	79.4175	862	3042	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	77.6209	328	3042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:22,237] [INFO] DFAST Taxonomy check result was written to GCF_000024005.1_ASM2400v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:22,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:22,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:22,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference/checkm_data
[2024-01-24 12:48:22,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:22,323] [INFO] Task started: CheckM
[2024-01-24 12:48:22,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024005.1_ASM2400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024005.1_ASM2400v1_genomic.fna/checkm_input GCF_000024005.1_ASM2400v1_genomic.fna/checkm_result
[2024-01-24 12:50:54,240] [INFO] Task succeeded: CheckM
[2024-01-24 12:50:54,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:50:54,269] [INFO] ===== Completeness check finished =====
[2024-01-24 12:50:54,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:50:54,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024005.1_ASM2400v1_genomic.fna/markers.fasta)
[2024-01-24 12:50:54,270] [INFO] Task started: Blastn
[2024-01-24 12:50:54,270] [INFO] Running command: blastn -query GCF_000024005.1_ASM2400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg420df19c-dffc-4cf4-9c5a-a01b58624301/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024005.1_ASM2400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:50:55,046] [INFO] Task succeeded: Blastn
[2024-01-24 12:50:55,049] [INFO] Selected 8 target genomes.
[2024-01-24 12:50:55,050] [INFO] Target genome list was writen to GCF_000024005.1_ASM2400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:50:55,077] [INFO] Task started: fastANI
[2024-01-24 12:50:55,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgc783ea28-75cc-400f-b2e7-65dd796782ce/GCF_000024005.1_ASM2400v1_genomic.fna.gz --refList GCF_000024005.1_ASM2400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024005.1_ASM2400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:51:10,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:10,981] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:51:10,981] [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_000024005.1	s__Chitinophaga pinensis	100.0	3041	3042	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_900114995.1	s__Chitinophaga sp900114995	90.2337	2649	3042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007896845.1	s__Chitinophaga pinensis_C	89.4794	2155	3042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093065.1	s__Chitinophaga agri	82.5973	1664	3042	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	81.182	1350	3042	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	81.1744	1413	3042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182155.1	s__Chitinophaga sp003182155	81.0549	1361	3042	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	80.7963	1379	3042	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 12:51:10,983] [INFO] GTDB search result was written to GCF_000024005.1_ASM2400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:51:10,984] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:51:10,986] [INFO] DFAST_QC result json was written to GCF_000024005.1_ASM2400v1_genomic.fna/dqc_result.json
[2024-01-24 12:51:10,986] [INFO] DFAST_QC completed!
[2024-01-24 12:51:10,986] [INFO] Total running time: 0h4m1s