[2023-06-28 00:27:48,912] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:27:48,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:27:48,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference
[2023-06-28 00:27:50,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:27:50,091] [INFO] Task started: Prodigal
[2023-06-28 00:27:50,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcfdae58-76ca-4e1f-a887-6ea556b3c5d4/GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:27:55,455] [INFO] Task succeeded: Prodigal
[2023-06-28 00:27:55,455] [INFO] Task started: HMMsearch
[2023-06-28 00:27:55,456] [INFO] Running command: hmmsearch --tblout GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference/reference_markers.hmm GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:27:55,676] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:27:55,678] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbcfdae58-76ca-4e1f-a887-6ea556b3c5d4/GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 00:27:55,704] [INFO] Query marker FASTA was written to GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 00:27:55,704] [INFO] Task started: Blastn
[2023-06-28 00:27:55,704] [INFO] Running command: blastn -query GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference/reference_markers.fasta -out GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:27:56,316] [INFO] Task succeeded: Blastn
[2023-06-28 00:27:56,321] [INFO] Selected 28 target genomes.
[2023-06-28 00:27:56,322] [INFO] Target genome list was writen to GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 00:27:56,330] [INFO] Task started: fastANI
[2023-06-28 00:27:56,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcfdae58-76ca-4e1f-a887-6ea556b3c5d4/GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:28:16,187] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:16,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:28:16,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:28:16,191] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:28:16,191] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:28:16,191] [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
--------------------------------------------------------------------------------
[2023-06-28 00:28:16,193] [INFO] DFAST Taxonomy check result was written to GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 00:28:16,194] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:28:16,195] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:28:16,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference/checkm_data
[2023-06-28 00:28:16,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:28:16,229] [INFO] Task started: CheckM
[2023-06-28 00:28:16,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 00:28:39,063] [INFO] Task succeeded: CheckM
[2023-06-28 00:28:39,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:28:39,088] [INFO] ===== Completeness check finished =====
[2023-06-28 00:28:39,089] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:28:39,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 00:28:39,089] [INFO] Task started: Blastn
[2023-06-28 00:28:39,090] [INFO] Running command: blastn -query GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg13da24c1-c689-48fc-aedd-bff62ceee425/dqc_reference/reference_markers_gtdb.fasta -out GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:39,899] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:39,904] [INFO] Selected 22 target genomes.
[2023-06-28 00:28:39,904] [INFO] Target genome list was writen to GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:28:39,933] [INFO] Task started: fastANI
[2023-06-28 00:28:39,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcfdae58-76ca-4e1f-a887-6ea556b3c5d4/GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:28:49,883] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:49,893] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:28:49,893] [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_000227505.4	s__Luminiphilus sp000227505	82.4402	482	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689915.1	s__Luminiphilus sp002689915	78.5122	197	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
GCA_003523185.1	s__Luminiphilus sp003523185	78.0422	126	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547755.1	s__Luminiphilus sp902547755	77.9873	86	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937065.1	s__Luminiphilus sp009937065	77.7519	94	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524755.1	s__Luminiphilus sp011524755	77.592	95	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_002691565.1	s__Luminiphilus sp002691565	77.2533	71	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
GCA_002469785.1	s__Luminiphilus sp002469785	77.1838	74	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:28:49,895] [INFO] GTDB search result was written to GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 00:28:49,895] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:28:49,899] [INFO] DFAST_QC result json was written to GCA_913063005.1_ERR771004_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 00:28:49,899] [INFO] DFAST_QC completed!
[2023-06-28 00:28:49,899] [INFO] Total running time: 0h1m1s