[2023-06-19 13:14:48,271] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:48,273] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:48,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference
[2023-06-19 13:14:49,429] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:49,430] [INFO] Task started: Prodigal
[2023-06-19 13:14:49,430] [INFO] Running command: gunzip -c /var/lib/cwl/stgc453ac62-42f0-4099-a23a-e369842630d5/GCA_018401735.1_ASM1840173v1_genomic.fna.gz | prodigal -d GCA_018401735.1_ASM1840173v1_genomic.fna/cds.fna -a GCA_018401735.1_ASM1840173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:15:00,356] [INFO] Task succeeded: Prodigal
[2023-06-19 13:15:00,356] [INFO] Task started: HMMsearch
[2023-06-19 13:15:00,356] [INFO] Running command: hmmsearch --tblout GCA_018401735.1_ASM1840173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference/reference_markers.hmm GCA_018401735.1_ASM1840173v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:15:00,542] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:15:00,543] [INFO] Found 6/6 markers.
[2023-06-19 13:15:00,570] [INFO] Query marker FASTA was written to GCA_018401735.1_ASM1840173v1_genomic.fna/markers.fasta
[2023-06-19 13:15:00,570] [INFO] Task started: Blastn
[2023-06-19 13:15:00,570] [INFO] Running command: blastn -query GCA_018401735.1_ASM1840173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference/reference_markers.fasta -out GCA_018401735.1_ASM1840173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:01,134] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:01,137] [INFO] Selected 29 target genomes.
[2023-06-19 13:15:01,138] [INFO] Target genome list was writen to GCA_018401735.1_ASM1840173v1_genomic.fna/target_genomes.txt
[2023-06-19 13:15:01,139] [INFO] Task started: fastANI
[2023-06-19 13:15:01,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgc453ac62-42f0-4099-a23a-e369842630d5/GCA_018401735.1_ASM1840173v1_genomic.fna.gz --refList GCA_018401735.1_ASM1840173v1_genomic.fna/target_genomes.txt --output GCA_018401735.1_ASM1840173v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:15:17,456] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:17,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:15:17,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:15:17,460] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:15:17,461] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:15:17,461] [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	76.4396	130	1022	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:15:17,468] [INFO] DFAST Taxonomy check result was written to GCA_018401735.1_ASM1840173v1_genomic.fna/tc_result.tsv
[2023-06-19 13:15:17,468] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:15:17,468] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:15:17,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference/checkm_data
[2023-06-19 13:15:17,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:15:17,500] [INFO] Task started: CheckM
[2023-06-19 13:15:17,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018401735.1_ASM1840173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018401735.1_ASM1840173v1_genomic.fna/checkm_input GCA_018401735.1_ASM1840173v1_genomic.fna/checkm_result
[2023-06-19 13:15:51,521] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:51,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:51,541] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:51,541] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:51,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018401735.1_ASM1840173v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:51,542] [INFO] Task started: Blastn
[2023-06-19 13:15:51,542] [INFO] Running command: blastn -query GCA_018401735.1_ASM1840173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg440fa368-e0c0-4782-8607-132c83bbf993/dqc_reference/reference_markers_gtdb.fasta -out GCA_018401735.1_ASM1840173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:52,300] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:52,304] [INFO] Selected 21 target genomes.
[2023-06-19 13:15:52,304] [INFO] Target genome list was writen to GCA_018401735.1_ASM1840173v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:52,312] [INFO] Task started: fastANI
[2023-06-19 13:15:52,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgc453ac62-42f0-4099-a23a-e369842630d5/GCA_018401735.1_ASM1840173v1_genomic.fna.gz --refList GCA_018401735.1_ASM1840173v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018401735.1_ASM1840173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:16:06,851] [INFO] Task succeeded: fastANI
[2023-06-19 13:16:06,857] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:16:06,857] [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
GCA_018401735.1	s__Croceimicrobium sp018401735	100.0	1017	1022	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_003045865.1	s__Croceimicrobium sp003045865	90.1871	795	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014524565.1	s__Croceimicrobium hydrocarbonivorans	76.4396	130	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795025.1	s__Croceimicrobium sp017795025	76.3889	130	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501205.1	s__Croceimicrobium sp002501205	76.34	123	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-19 13:16:06,859] [INFO] GTDB search result was written to GCA_018401735.1_ASM1840173v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:16:06,859] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:16:06,862] [INFO] DFAST_QC result json was written to GCA_018401735.1_ASM1840173v1_genomic.fna/dqc_result.json
[2023-06-19 13:16:06,862] [INFO] DFAST_QC completed!
[2023-06-19 13:16:06,862] [INFO] Total running time: 0h1m19s