[2023-06-28 01:18:10,746] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:18:10,763] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:18:10,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference
[2023-06-28 01:18:12,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:18:12,139] [INFO] Task started: Prodigal
[2023-06-28 01:18:12,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg946b7e0e-d75a-470e-acb6-aad6846b3a24/GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:18:24,385] [INFO] Task succeeded: Prodigal
[2023-06-28 01:18:24,385] [INFO] Task started: HMMsearch
[2023-06-28 01:18:24,386] [INFO] Running command: hmmsearch --tblout GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference/reference_markers.hmm GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:18:24,691] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:18:24,692] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg946b7e0e-d75a-470e-acb6-aad6846b3a24/GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 01:18:24,737] [INFO] Query marker FASTA was written to GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 01:18:24,738] [INFO] Task started: Blastn
[2023-06-28 01:18:24,738] [INFO] Running command: blastn -query GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference/reference_markers.fasta -out GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:18:25,433] [INFO] Task succeeded: Blastn
[2023-06-28 01:18:25,438] [INFO] Selected 22 target genomes.
[2023-06-28 01:18:25,438] [INFO] Target genome list was writen to GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 01:18:25,441] [INFO] Task started: fastANI
[2023-06-28 01:18:25,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg946b7e0e-d75a-470e-acb6-aad6846b3a24/GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:18:40,628] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:40,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:18:40,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:18:40,636] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:18:40,636] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:18:40,636] [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
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	77.9698	195	1502	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	77.9551	206	1502	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	77.1404	93	1502	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	77.0788	93	1502	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	77.0788	93	1502	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.2101	71	1502	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:18:40,638] [INFO] DFAST Taxonomy check result was written to GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 01:18:40,639] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:18:40,639] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:18:40,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference/checkm_data
[2023-06-28 01:18:40,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:18:40,686] [INFO] Task started: CheckM
[2023-06-28 01:18:40,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 01:19:21,287] [INFO] Task succeeded: CheckM
[2023-06-28 01:19:21,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:19:21,312] [INFO] ===== Completeness check finished =====
[2023-06-28 01:19:21,312] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:19:21,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 01:19:21,313] [INFO] Task started: Blastn
[2023-06-28 01:19:21,313] [INFO] Running command: blastn -query GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddf12cb-c48e-4b7e-b809-1f5056319430/dqc_reference/reference_markers_gtdb.fasta -out GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:19:22,389] [INFO] Task succeeded: Blastn
[2023-06-28 01:19:22,394] [INFO] Selected 20 target genomes.
[2023-06-28 01:19:22,395] [INFO] Target genome list was writen to GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:19:22,419] [INFO] Task started: fastANI
[2023-06-28 01:19:22,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg946b7e0e-d75a-470e-acb6-aad6846b3a24/GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:19:36,332] [INFO] Task succeeded: fastANI
[2023-06-28 01:19:36,343] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:19:36,344] [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_002707785.1	s__Pseudomaricurvus sp002707785	99.8274	1399	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	99.83	99.83	0.94	0.94	2	conclusive
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	77.9625	196	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	77.9551	206	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	77.7828	200	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	77.3387	112	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	77.1134	91	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_000377745.1	s__Gilvimarinus chinensis	76.2317	69	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	76.1168	57	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363885.1	s__Cellvibrio sp004363885	75.9782	57	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:19:36,346] [INFO] GTDB search result was written to GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 01:19:36,346] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:19:36,349] [INFO] DFAST_QC result json was written to GCA_913044175.1_ERR599044_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 01:19:36,349] [INFO] DFAST_QC completed!
[2023-06-28 01:19:36,350] [INFO] Total running time: 0h1m26s