[2024-01-25 18:02:50,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:50,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:50,528] [INFO] DQC Reference Directory: /var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference
[2024-01-25 18:02:51,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:51,629] [INFO] Task started: Prodigal
[2024-01-25 18:02:51,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg700bea5c-5c49-45c7-bbef-8e65b5350a5b/GCF_014524565.1_ASM1452456v1_genomic.fna.gz | prodigal -d GCF_014524565.1_ASM1452456v1_genomic.fna/cds.fna -a GCF_014524565.1_ASM1452456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:05,738] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:05,738] [INFO] Task started: HMMsearch
[2024-01-25 18:03:05,739] [INFO] Running command: hmmsearch --tblout GCF_014524565.1_ASM1452456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference/reference_markers.hmm GCF_014524565.1_ASM1452456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:06,017] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:06,020] [INFO] Found 6/6 markers.
[2024-01-25 18:03:06,061] [INFO] Query marker FASTA was written to GCF_014524565.1_ASM1452456v1_genomic.fna/markers.fasta
[2024-01-25 18:03:06,061] [INFO] Task started: Blastn
[2024-01-25 18:03:06,062] [INFO] Running command: blastn -query GCF_014524565.1_ASM1452456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference/reference_markers.fasta -out GCF_014524565.1_ASM1452456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:06,623] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:06,626] [INFO] Selected 26 target genomes.
[2024-01-25 18:03:06,626] [INFO] Target genome list was writen to GCF_014524565.1_ASM1452456v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:06,637] [INFO] Task started: fastANI
[2024-01-25 18:03:06,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg700bea5c-5c49-45c7-bbef-8e65b5350a5b/GCF_014524565.1_ASM1452456v1_genomic.fna.gz --refList GCF_014524565.1_ASM1452456v1_genomic.fna/target_genomes.txt --output GCF_014524565.1_ASM1452456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:22,781] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:22,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:22,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:22,786] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:22,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:22,786] [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
Croceimicrobium hydrocarbonivorans	strain=A20-9	GCA_014524565.1	2761580	2761580	type	True	100.0	1344	1345	95	conclusive
Owenweeksia hongkongensis	strain=DSM 17368	GCA_000236705.1	253245	253245	type	True	76.7431	65	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:22,790] [INFO] DFAST Taxonomy check result was written to GCF_014524565.1_ASM1452456v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:22,790] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:22,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:22,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference/checkm_data
[2024-01-25 18:03:22,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:22,833] [INFO] Task started: CheckM
[2024-01-25 18:03:22,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014524565.1_ASM1452456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014524565.1_ASM1452456v1_genomic.fna/checkm_input GCF_014524565.1_ASM1452456v1_genomic.fna/checkm_result
[2024-01-25 18:04:04,516] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:04,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:04,532] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:04,532] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:04,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014524565.1_ASM1452456v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:04,533] [INFO] Task started: Blastn
[2024-01-25 18:04:04,533] [INFO] Running command: blastn -query GCF_014524565.1_ASM1452456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb236019f-33b4-459c-bd70-d31e19a885b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014524565.1_ASM1452456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:05,331] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:05,334] [INFO] Selected 19 target genomes.
[2024-01-25 18:04:05,334] [INFO] Target genome list was writen to GCF_014524565.1_ASM1452456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:05,362] [INFO] Task started: fastANI
[2024-01-25 18:04:05,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg700bea5c-5c49-45c7-bbef-8e65b5350a5b/GCF_014524565.1_ASM1452456v1_genomic.fna.gz --refList GCF_014524565.1_ASM1452456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014524565.1_ASM1452456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:17,674] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:17,678] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:17,678] [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_014524565.1	s__Croceimicrobium hydrocarbonivorans	100.0	1344	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002501205.1	s__Croceimicrobium sp002501205	90.595	1039	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
GCA_017795025.1	s__Croceimicrobium sp017795025	78.1961	373	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401735.1	s__Croceimicrobium sp018401735	76.8895	118	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045865.1	s__Croceimicrobium sp003045865	76.8459	126	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:17,680] [INFO] GTDB search result was written to GCF_014524565.1_ASM1452456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:17,680] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:17,682] [INFO] DFAST_QC result json was written to GCF_014524565.1_ASM1452456v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:17,682] [INFO] DFAST_QC completed!
[2024-01-25 18:04:17,682] [INFO] Total running time: 0h1m27s