[2023-06-29 16:19:16,950] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:19:16,954] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:19:16,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference
[2023-06-29 16:19:18,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:19:18,301] [INFO] Task started: Prodigal
[2023-06-29 16:19:18,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg940318fc-5a23-4864-ad02-ec28cea460c4/GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:19:28,600] [INFO] Task succeeded: Prodigal
[2023-06-29 16:19:28,601] [INFO] Task started: HMMsearch
[2023-06-29 16:19:28,601] [INFO] Running command: hmmsearch --tblout GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference/reference_markers.hmm GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:19:28,921] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:19:28,922] [INFO] Found 6/6 markers.
[2023-06-29 16:19:28,951] [INFO] Query marker FASTA was written to GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:19:28,951] [INFO] Task started: Blastn
[2023-06-29 16:19:28,951] [INFO] Running command: blastn -query GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference/reference_markers.fasta -out GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:29,542] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:29,546] [INFO] Selected 21 target genomes.
[2023-06-29 16:19:29,546] [INFO] Target genome list was writen to GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:19:29,550] [INFO] Task started: fastANI
[2023-06-29 16:19:29,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg940318fc-5a23-4864-ad02-ec28cea460c4/GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:19:45,220] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:45,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:19:45,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:19:45,224] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:19:45,224] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:19:45,224] [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
--------------------------------------------------------------------------------
[2023-06-29 16:19:45,227] [INFO] DFAST Taxonomy check result was written to GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:19:45,227] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:19:45,228] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:19:45,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference/checkm_data
[2023-06-29 16:19:45,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:19:45,278] [INFO] Task started: CheckM
[2023-06-29 16:19:45,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:20:20,633] [INFO] Task succeeded: CheckM
[2023-06-29 16:20:20,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:20:20,655] [INFO] ===== Completeness check finished =====
[2023-06-29 16:20:20,656] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:20:20,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:20:20,657] [INFO] Task started: Blastn
[2023-06-29 16:20:20,657] [INFO] Running command: blastn -query GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg84dbd3e4-0869-4371-9441-1e6170a6847a/dqc_reference/reference_markers_gtdb.fasta -out GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:20:21,401] [INFO] Task succeeded: Blastn
[2023-06-29 16:20:21,406] [INFO] Selected 19 target genomes.
[2023-06-29 16:20:21,407] [INFO] Target genome list was writen to GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:20:21,415] [INFO] Task started: fastANI
[2023-06-29 16:20:21,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg940318fc-5a23-4864-ad02-ec28cea460c4/GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:20:29,571] [INFO] Task succeeded: fastANI
[2023-06-29 16:20:29,585] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:20:29,585] [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_001897515.1	s__Bact-08 sp001897515	99.9982	796	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018053445.1	s__Bact-08 sp018053445	79.6024	274	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	99.49	99.40	0.91	0.88	5	-
GCA_002842695.1	s__Bact-08 sp002842695	77.6587	175	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842655.1	s__Bact-08 sp002842655	77.3062	156	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860395.1	s__Bact-08 sp017860395	77.0667	69	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840895.1	s__Bact-08 sp002840895	76.9342	79	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842515.1	s__Bact-08 sp002842515	76.8545	78	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	98.10	97.95	0.94	0.90	6	-
GCA_002425935.1	s__Bact-08 sp002425935	76.7479	79	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-08	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:20:29,587] [INFO] GTDB search result was written to GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:20:29,588] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:20:29,591] [INFO] DFAST_QC result json was written to GCA_937973865.1_SRR3901694_bin.22_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:20:29,591] [INFO] DFAST_QC completed!
[2023-06-29 16:20:29,591] [INFO] Total running time: 0h1m13s