[2023-06-16 23:29:46,356] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:29:46,375] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:29:46,375] [INFO] DQC Reference Directory: /var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference
[2023-06-16 23:29:50,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:29:50,143] [INFO] Task started: Prodigal
[2023-06-16 23:29:50,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg71b39e7e-07a7-48b2-8ee4-ec47443eb9a5/GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna.gz | prodigal -d GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/cds.fna -a GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:29:52,077] [INFO] Task succeeded: Prodigal
[2023-06-16 23:29:52,077] [INFO] Task started: HMMsearch
[2023-06-16 23:29:52,077] [INFO] Running command: hmmsearch --tblout GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference/reference_markers.hmm GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:29:52,327] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:29:52,329] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg71b39e7e-07a7-48b2-8ee4-ec47443eb9a5/GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna.gz]
[2023-06-16 23:29:52,354] [INFO] Query marker FASTA was written to GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/markers.fasta
[2023-06-16 23:29:52,354] [INFO] Task started: Blastn
[2023-06-16 23:29:52,355] [INFO] Running command: blastn -query GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/markers.fasta -db /var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference/reference_markers.fasta -out GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:29:54,161] [INFO] Task succeeded: Blastn
[2023-06-16 23:29:54,169] [INFO] Selected 11 target genomes.
[2023-06-16 23:29:54,170] [INFO] Target genome list was writen to GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/target_genomes.txt
[2023-06-16 23:29:54,173] [INFO] Task started: fastANI
[2023-06-16 23:29:54,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b39e7e-07a7-48b2-8ee4-ec47443eb9a5/GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna.gz --refList GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/target_genomes.txt --output GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:29:59,565] [INFO] Task succeeded: fastANI
[2023-06-16 23:29:59,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:29:59,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:29:59,568] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:29:59,568] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 23:29:59,568] [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
--------------------------------------------------------------------------------
[2023-06-16 23:29:59,570] [INFO] DFAST Taxonomy check result was written to GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/tc_result.tsv
[2023-06-16 23:29:59,571] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:29:59,571] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:29:59,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference/checkm_data
[2023-06-16 23:29:59,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:29:59,591] [INFO] Task started: CheckM
[2023-06-16 23:29:59,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/checkm_input GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/checkm_result
[2023-06-16 23:30:14,599] [INFO] Task succeeded: CheckM
[2023-06-16 23:30:14,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:30:14,623] [INFO] ===== Completeness check finished =====
[2023-06-16 23:30:14,623] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:30:14,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/markers.fasta)
[2023-06-16 23:30:14,624] [INFO] Task started: Blastn
[2023-06-16 23:30:14,624] [INFO] Running command: blastn -query GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/markers.fasta -db /var/lib/cwl/stga8097ba2-4c01-42e4-b6f9-dcff20b0ace5/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:30:15,395] [INFO] Task succeeded: Blastn
[2023-06-16 23:30:15,399] [INFO] Selected 7 target genomes.
[2023-06-16 23:30:15,399] [INFO] Target genome list was writen to GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:30:15,401] [INFO] Task started: fastANI
[2023-06-16 23:30:15,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b39e7e-07a7-48b2-8ee4-ec47443eb9a5/GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna.gz --refList GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/target_genomes_gtdb.txt --output GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:30:17,442] [INFO] Task succeeded: fastANI
[2023-06-16 23:30:17,457] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 23:30:17,457] [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_900552555.1	s__CAG-269 sp900552555	87.2661	153	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900753165.1	s__CAG-269 sp900753165	87.1384	138	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.76	0.76	2	-
GCA_001916065.1	s__CAG-269 sp001916065	86.6215	157	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.24	97.60	0.86	0.82	5	-
GCA_000438255.1	s__CAG-269 sp000438255	85.9514	145	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	-
GCA_900551615.1	s__CAG-269 sp900551615	85.7638	148	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_001916005.1	s__CAG-269 sp001916005	83.1246	146	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
GCA_904384205.1	s__CAG-269 sp904384205	79.8634	106	251	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:30:17,459] [INFO] GTDB search result was written to GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/result_gtdb.tsv
[2023-06-16 23:30:17,460] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:30:17,462] [INFO] DFAST_QC result json was written to GCA_905201225.1_ERR321564-mag-bin.30_genomic.fna/dqc_result.json
[2023-06-16 23:30:17,462] [INFO] DFAST_QC completed!
[2023-06-16 23:30:17,463] [INFO] Total running time: 0h0m31s