[2023-06-13 01:02:19,447] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:02:19,458] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:02:19,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference
[2023-06-13 01:02:20,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:02:20,742] [INFO] Task started: Prodigal
[2023-06-13 01:02:20,742] [INFO] Running command: gunzip -c /var/lib/cwl/stgef074918-1f9b-4c23-814b-3f2ea68b310b/GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:02:28,205] [INFO] Task succeeded: Prodigal
[2023-06-13 01:02:28,205] [INFO] Task started: HMMsearch
[2023-06-13 01:02:28,206] [INFO] Running command: hmmsearch --tblout GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference/reference_markers.hmm GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:02:28,461] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:02:28,462] [INFO] Found 6/6 markers.
[2023-06-13 01:02:28,487] [INFO] Query marker FASTA was written to GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 01:02:28,488] [INFO] Task started: Blastn
[2023-06-13 01:02:28,488] [INFO] Running command: blastn -query GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference/reference_markers.fasta -out GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:02:29,137] [INFO] Task succeeded: Blastn
[2023-06-13 01:02:29,141] [INFO] Selected 26 target genomes.
[2023-06-13 01:02:29,142] [INFO] Target genome list was writen to GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 01:02:29,146] [INFO] Task started: fastANI
[2023-06-13 01:02:29,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgef074918-1f9b-4c23-814b-3f2ea68b310b/GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:02:48,033] [INFO] Task succeeded: fastANI
[2023-06-13 01:02:48,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:02:48,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:02:48,040] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:02:48,040] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:02:48,040] [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
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	75.0133	56	885	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	74.9428	54	885	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	74.9428	54	885	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	74.8051	57	885	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7715	67	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:02:48,042] [INFO] DFAST Taxonomy check result was written to GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 01:02:48,043] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:02:48,043] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:02:48,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference/checkm_data
[2023-06-13 01:02:48,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:02:48,078] [INFO] Task started: CheckM
[2023-06-13 01:02:48,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 01:03:15,442] [INFO] Task succeeded: CheckM
[2023-06-13 01:03:15,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:03:15,466] [INFO] ===== Completeness check finished =====
[2023-06-13 01:03:15,466] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:03:15,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 01:03:15,467] [INFO] Task started: Blastn
[2023-06-13 01:03:15,467] [INFO] Running command: blastn -query GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9fcab7b-6598-4675-a493-8ed70b3bf27d/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:03:16,492] [INFO] Task succeeded: Blastn
[2023-06-13 01:03:16,497] [INFO] Selected 10 target genomes.
[2023-06-13 01:03:16,498] [INFO] Target genome list was writen to GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:03:16,530] [INFO] Task started: fastANI
[2023-06-13 01:03:16,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgef074918-1f9b-4c23-814b-3f2ea68b310b/GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:03:22,119] [INFO] Task succeeded: fastANI
[2023-06-13 01:03:22,127] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 01:03:22,128] [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_900542395.1	s__Ventricola sp900542395	97.7504	630	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.33	97.06	0.84	0.79	5	conclusive
GCA_900542445.1	s__Ventricola sp900542445	87.3024	636	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	98.97	98.40	0.91	0.87	4	-
GCA_900548125.1	s__Ventricola sp900548125	83.5945	375	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.02	96.93	0.87	0.87	4	-
GCA_004556985.1	s__Ventricola sp004556985	81.4253	391	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555535.1	s__Ventricola sp004555535	81.2861	431	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937505.1	s__Ventricola sp017937505	80.711	408	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716525.1	s__Ventricola gallistercoris	80.3412	335	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056305.1	s__Ventricola sp015056305	79.6968	307	885	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:03:22,130] [INFO] GTDB search result was written to GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 01:03:22,130] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:03:22,133] [INFO] DFAST_QC result json was written to GCA_938005175.1_ERR1600584_bin.27_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 01:03:22,133] [INFO] DFAST_QC completed!
[2023-06-13 01:03:22,133] [INFO] Total running time: 0h1m3s