[2023-06-28 12:27:48,463] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:27:48,466] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:27:48,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference
[2023-06-28 12:27:50,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:27:50,725] [INFO] Task started: Prodigal
[2023-06-28 12:27:50,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ee8e48c-eb81-48d0-9904-565ef039552f/GCA_020528935.1_ASM2052893v1_genomic.fna.gz | prodigal -d GCA_020528935.1_ASM2052893v1_genomic.fna/cds.fna -a GCA_020528935.1_ASM2052893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:28:10,866] [INFO] Task succeeded: Prodigal
[2023-06-28 12:28:10,866] [INFO] Task started: HMMsearch
[2023-06-28 12:28:10,867] [INFO] Running command: hmmsearch --tblout GCA_020528935.1_ASM2052893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference/reference_markers.hmm GCA_020528935.1_ASM2052893v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:28:11,105] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:28:11,107] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9ee8e48c-eb81-48d0-9904-565ef039552f/GCA_020528935.1_ASM2052893v1_genomic.fna.gz]
[2023-06-28 12:28:11,142] [INFO] Query marker FASTA was written to GCA_020528935.1_ASM2052893v1_genomic.fna/markers.fasta
[2023-06-28 12:28:11,143] [INFO] Task started: Blastn
[2023-06-28 12:28:11,143] [INFO] Running command: blastn -query GCA_020528935.1_ASM2052893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference/reference_markers.fasta -out GCA_020528935.1_ASM2052893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:28:11,784] [INFO] Task succeeded: Blastn
[2023-06-28 12:28:11,789] [INFO] Selected 20 target genomes.
[2023-06-28 12:28:11,789] [INFO] Target genome list was writen to GCA_020528935.1_ASM2052893v1_genomic.fna/target_genomes.txt
[2023-06-28 12:28:11,794] [INFO] Task started: fastANI
[2023-06-28 12:28:11,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee8e48c-eb81-48d0-9904-565ef039552f/GCA_020528935.1_ASM2052893v1_genomic.fna.gz --refList GCA_020528935.1_ASM2052893v1_genomic.fna/target_genomes.txt --output GCA_020528935.1_ASM2052893v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:28:24,148] [INFO] Task succeeded: fastANI
[2023-06-28 12:28:24,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:28:24,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:28:24,160] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:28:24,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:28:24,160] [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
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	76.1506	63	885	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	76.1506	63	885	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.9238	53	885	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	75.7647	52	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:28:24,164] [INFO] DFAST Taxonomy check result was written to GCA_020528935.1_ASM2052893v1_genomic.fna/tc_result.tsv
[2023-06-28 12:28:24,165] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:28:24,165] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:28:24,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference/checkm_data
[2023-06-28 12:28:24,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:28:24,208] [INFO] Task started: CheckM
[2023-06-28 12:28:24,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020528935.1_ASM2052893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020528935.1_ASM2052893v1_genomic.fna/checkm_input GCA_020528935.1_ASM2052893v1_genomic.fna/checkm_result
[2023-06-28 12:29:19,201] [INFO] Task succeeded: CheckM
[2023-06-28 12:29:19,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:29:19,233] [INFO] ===== Completeness check finished =====
[2023-06-28 12:29:19,233] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:29:19,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020528935.1_ASM2052893v1_genomic.fna/markers.fasta)
[2023-06-28 12:29:19,234] [INFO] Task started: Blastn
[2023-06-28 12:29:19,235] [INFO] Running command: blastn -query GCA_020528935.1_ASM2052893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0824c218-1636-4ed0-bf9c-8c32728c2932/dqc_reference/reference_markers_gtdb.fasta -out GCA_020528935.1_ASM2052893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:29:20,222] [INFO] Task succeeded: Blastn
[2023-06-28 12:29:20,227] [INFO] Selected 23 target genomes.
[2023-06-28 12:29:20,227] [INFO] Target genome list was writen to GCA_020528935.1_ASM2052893v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:29:20,240] [INFO] Task started: fastANI
[2023-06-28 12:29:20,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee8e48c-eb81-48d0-9904-565ef039552f/GCA_020528935.1_ASM2052893v1_genomic.fna.gz --refList GCA_020528935.1_ASM2052893v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020528935.1_ASM2052893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:29:34,448] [INFO] Task succeeded: fastANI
[2023-06-28 12:29:34,458] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:29:34,458] [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_015490175.1	s__WFYJ01 sp015490175	76.3551	101	885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	76.1506	63	885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803465.1	s__Lewinella_A litorea	75.9238	53	885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	75.8945	67	885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360405.1	s__JABWBR01 sp013360405	75.7639	57	885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:29:34,460] [INFO] GTDB search result was written to GCA_020528935.1_ASM2052893v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:29:34,461] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:29:34,464] [INFO] DFAST_QC result json was written to GCA_020528935.1_ASM2052893v1_genomic.fna/dqc_result.json
[2023-06-28 12:29:34,464] [INFO] DFAST_QC completed!
[2023-06-28 12:29:34,464] [INFO] Total running time: 0h1m46s