[2024-01-24 11:20:34,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference
[2024-01-24 11:20:35,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,375] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fc084d9-d9bd-4206-ab0a-65057271c73a/GCF_021234875.1_ASM2123487v1_genomic.fna.gz | prodigal -d GCF_021234875.1_ASM2123487v1_genomic.fna/cds.fna -a GCF_021234875.1_ASM2123487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:48,238] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:48,238] [INFO] Task started: HMMsearch
[2024-01-24 11:20:48,239] [INFO] Running command: hmmsearch --tblout GCF_021234875.1_ASM2123487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference/reference_markers.hmm GCF_021234875.1_ASM2123487v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:48,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:48,518] [INFO] Found 6/6 markers.
[2024-01-24 11:20:48,558] [INFO] Query marker FASTA was written to GCF_021234875.1_ASM2123487v1_genomic.fna/markers.fasta
[2024-01-24 11:20:48,559] [INFO] Task started: Blastn
[2024-01-24 11:20:48,559] [INFO] Running command: blastn -query GCF_021234875.1_ASM2123487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference/reference_markers.fasta -out GCF_021234875.1_ASM2123487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:49,209] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:49,212] [INFO] Selected 25 target genomes.
[2024-01-24 11:20:49,213] [INFO] Target genome list was writen to GCF_021234875.1_ASM2123487v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:49,232] [INFO] Task started: fastANI
[2024-01-24 11:20:49,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc084d9-d9bd-4206-ab0a-65057271c73a/GCF_021234875.1_ASM2123487v1_genomic.fna.gz --refList GCF_021234875.1_ASM2123487v1_genomic.fna/target_genomes.txt --output GCF_021234875.1_ASM2123487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:03,003] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:03,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:03,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:03,011] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:03,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:03,011] [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
Marinibactrum halimedae	strain=NBRC 110095	GCA_021234875.1	1444977	1444977	type	True	100.0	1643	1652	95	conclusive
Sessilibacter corallicola	strain=C21	GCA_021290925.1	2904075	2904075	type	True	77.0079	67	1652	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	76.6404	52	1652	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.5279	51	1652	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.4826	50	1652	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	76.374	52	1652	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	75.7247	53	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:03,013] [INFO] DFAST Taxonomy check result was written to GCF_021234875.1_ASM2123487v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:03,014] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:03,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:03,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference/checkm_data
[2024-01-24 11:21:03,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:03,067] [INFO] Task started: CheckM
[2024-01-24 11:21:03,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021234875.1_ASM2123487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021234875.1_ASM2123487v1_genomic.fna/checkm_input GCF_021234875.1_ASM2123487v1_genomic.fna/checkm_result
[2024-01-24 11:21:44,600] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:44,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:44,628] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:44,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:44,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021234875.1_ASM2123487v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:44,629] [INFO] Task started: Blastn
[2024-01-24 11:21:44,629] [INFO] Running command: blastn -query GCF_021234875.1_ASM2123487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20500828-dfda-44c2-950b-ae5b803aae33/dqc_reference/reference_markers_gtdb.fasta -out GCF_021234875.1_ASM2123487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:45,624] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:45,628] [INFO] Selected 34 target genomes.
[2024-01-24 11:21:45,628] [INFO] Target genome list was writen to GCF_021234875.1_ASM2123487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:45,653] [INFO] Task started: fastANI
[2024-01-24 11:21:45,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc084d9-d9bd-4206-ab0a-65057271c73a/GCF_021234875.1_ASM2123487v1_genomic.fna.gz --refList GCF_021234875.1_ASM2123487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021234875.1_ASM2123487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:05,768] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:05,775] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:22:05,775] [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_000013665.1	s__Saccharophagus degradans	76.658	53	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	76.4826	50	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_902141825.1	s__Thalassocella blandensis	76.2551	51	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Thalassocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	75.7247	53	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:05,776] [INFO] GTDB search result was written to GCF_021234875.1_ASM2123487v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:05,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:05,779] [INFO] DFAST_QC result json was written to GCF_021234875.1_ASM2123487v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:05,780] [INFO] DFAST_QC completed!
[2024-01-24 11:22:05,780] [INFO] Total running time: 0h1m32s