[2024-01-24 14:05:36,020] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,021] [INFO] DQC Reference Directory: /var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference
[2024-01-24 14:05:37,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,416] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,416] [INFO] Running command: gunzip -c /var/lib/cwl/stgeecf0888-8aad-478d-91d3-0145f38de746/GCF_004803465.1_ASM480346v1_genomic.fna.gz | prodigal -d GCF_004803465.1_ASM480346v1_genomic.fna/cds.fna -a GCF_004803465.1_ASM480346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:01,610] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:01,611] [INFO] Task started: HMMsearch
[2024-01-24 14:06:01,611] [INFO] Running command: hmmsearch --tblout GCF_004803465.1_ASM480346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference/reference_markers.hmm GCF_004803465.1_ASM480346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:01,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:01,932] [INFO] Found 6/6 markers.
[2024-01-24 14:06:01,973] [INFO] Query marker FASTA was written to GCF_004803465.1_ASM480346v1_genomic.fna/markers.fasta
[2024-01-24 14:06:01,974] [INFO] Task started: Blastn
[2024-01-24 14:06:01,974] [INFO] Running command: blastn -query GCF_004803465.1_ASM480346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference/reference_markers.fasta -out GCF_004803465.1_ASM480346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:02,627] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:02,631] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:02,631] [INFO] Target genome list was writen to GCF_004803465.1_ASM480346v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:02,643] [INFO] Task started: fastANI
[2024-01-24 14:06:02,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgeecf0888-8aad-478d-91d3-0145f38de746/GCF_004803465.1_ASM480346v1_genomic.fna.gz --refList GCF_004803465.1_ASM480346v1_genomic.fna/target_genomes.txt --output GCF_004803465.1_ASM480346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:12,624] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:12,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:12,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:12,633] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:12,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:12,633] [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 litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	100.0	1447	1449	95	conclusive
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	83.4967	1133	1449	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	83.4219	1135	1449	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	78.8483	634	1449	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	78.6576	586	1449	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	78.6278	610	1449	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.3522	53	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:12,634] [INFO] DFAST Taxonomy check result was written to GCF_004803465.1_ASM480346v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:12,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:12,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:12,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference/checkm_data
[2024-01-24 14:06:12,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:12,683] [INFO] Task started: CheckM
[2024-01-24 14:06:12,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004803465.1_ASM480346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004803465.1_ASM480346v1_genomic.fna/checkm_input GCF_004803465.1_ASM480346v1_genomic.fna/checkm_result
[2024-01-24 14:07:18,288] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:18,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:18,309] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:18,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:18,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004803465.1_ASM480346v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:18,311] [INFO] Task started: Blastn
[2024-01-24 14:07:18,311] [INFO] Running command: blastn -query GCF_004803465.1_ASM480346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaada46a2-824e-4fbc-ad4c-a1c030833924/dqc_reference/reference_markers_gtdb.fasta -out GCF_004803465.1_ASM480346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:19,159] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:19,163] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:19,163] [INFO] Target genome list was writen to GCF_004803465.1_ASM480346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:19,172] [INFO] Task started: fastANI
[2024-01-24 14:07:19,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgeecf0888-8aad-478d-91d3-0145f38de746/GCF_004803465.1_ASM480346v1_genomic.fna.gz --refList GCF_004803465.1_ASM480346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004803465.1_ASM480346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:27,665] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:27,678] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:27,678] [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_004803465.1	s__Lewinella_A litorea	100.0	1447	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002631205.1	s__Lewinella_A marina	83.4967	1133	1449	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_003390915.1	s__Lewinella_A sp003390915	79.9213	830	1449	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_014197245.1	s__Lewinella_A aquimaris	78.8282	637	1449	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_003390935.1	s__Lewinella_A sp003390935	78.7119	573	1449	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_002934605.1	s__Lewinella_A xylanilytica	78.6546	606	1449	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_014349155.1	s__Lewinella_A lacunae	77.1498	293	1449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:27,680] [INFO] GTDB search result was written to GCF_004803465.1_ASM480346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:27,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:27,683] [INFO] DFAST_QC result json was written to GCF_004803465.1_ASM480346v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:27,683] [INFO] DFAST_QC completed!
[2024-01-24 14:07:27,683] [INFO] Total running time: 0h1m52s