[2023-06-05 18:56:58,031] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:58,040] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:58,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference
[2023-06-05 18:56:59,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:59,186] [INFO] Task started: Prodigal
[2023-06-05 18:56:59,186] [INFO] Running command: gunzip -c /var/lib/cwl/stgaccbf1e7-cfb5-434b-9e22-3cbdeb64ebe1/GCA_934167375.1_ERR7738563_bin.172_genomic.fna.gz | prodigal -d GCA_934167375.1_ERR7738563_bin.172_genomic.fna/cds.fna -a GCA_934167375.1_ERR7738563_bin.172_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:01,145] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:01,145] [INFO] Task started: HMMsearch
[2023-06-05 18:57:01,145] [INFO] Running command: hmmsearch --tblout GCA_934167375.1_ERR7738563_bin.172_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference/reference_markers.hmm GCA_934167375.1_ERR7738563_bin.172_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:01,305] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:01,306] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaccbf1e7-cfb5-434b-9e22-3cbdeb64ebe1/GCA_934167375.1_ERR7738563_bin.172_genomic.fna.gz]
[2023-06-05 18:57:01,325] [INFO] Query marker FASTA was written to GCA_934167375.1_ERR7738563_bin.172_genomic.fna/markers.fasta
[2023-06-05 18:57:01,325] [INFO] Task started: Blastn
[2023-06-05 18:57:01,325] [INFO] Running command: blastn -query GCA_934167375.1_ERR7738563_bin.172_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference/reference_markers.fasta -out GCA_934167375.1_ERR7738563_bin.172_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:01,803] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:01,806] [INFO] Selected 10 target genomes.
[2023-06-05 18:57:01,806] [INFO] Target genome list was writen to GCA_934167375.1_ERR7738563_bin.172_genomic.fna/target_genomes.txt
[2023-06-05 18:57:01,807] [INFO] Task started: fastANI
[2023-06-05 18:57:01,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgaccbf1e7-cfb5-434b-9e22-3cbdeb64ebe1/GCA_934167375.1_ERR7738563_bin.172_genomic.fna.gz --refList GCA_934167375.1_ERR7738563_bin.172_genomic.fna/target_genomes.txt --output GCA_934167375.1_ERR7738563_bin.172_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:06,914] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:06,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:06,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:06,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:06,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:57:06,916] [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
--------------------------------------------------------------------------------
[2023-06-05 18:57:06,918] [INFO] DFAST Taxonomy check result was written to GCA_934167375.1_ERR7738563_bin.172_genomic.fna/tc_result.tsv
[2023-06-05 18:57:06,919] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:06,920] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:06,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference/checkm_data
[2023-06-05 18:57:06,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:06,940] [INFO] Task started: CheckM
[2023-06-05 18:57:06,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934167375.1_ERR7738563_bin.172_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934167375.1_ERR7738563_bin.172_genomic.fna/checkm_input GCA_934167375.1_ERR7738563_bin.172_genomic.fna/checkm_result
[2023-06-05 18:57:19,569] [INFO] Task succeeded: CheckM
[2023-06-05 18:57:19,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.08%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:57:19,587] [INFO] ===== Completeness check finished =====
[2023-06-05 18:57:19,587] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:57:19,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934167375.1_ERR7738563_bin.172_genomic.fna/markers.fasta)
[2023-06-05 18:57:19,587] [INFO] Task started: Blastn
[2023-06-05 18:57:19,588] [INFO] Running command: blastn -query GCA_934167375.1_ERR7738563_bin.172_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a26e533-798b-4f60-9deb-713d75e92da9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934167375.1_ERR7738563_bin.172_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:20,147] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:20,150] [INFO] Selected 12 target genomes.
[2023-06-05 18:57:20,150] [INFO] Target genome list was writen to GCA_934167375.1_ERR7738563_bin.172_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:57:20,153] [INFO] Task started: fastANI
[2023-06-05 18:57:20,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgaccbf1e7-cfb5-434b-9e22-3cbdeb64ebe1/GCA_934167375.1_ERR7738563_bin.172_genomic.fna.gz --refList GCA_934167375.1_ERR7738563_bin.172_genomic.fna/target_genomes_gtdb.txt --output GCA_934167375.1_ERR7738563_bin.172_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:57:23,289] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:23,298] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:57:23,298] [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_900556345.1	s__CAG-269 sp900556345	87.1848	171	372	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	97.06	97.06	0.82	0.82	2	-
GCA_900553125.1	s__CAG-269 sp900553125	86.0687	246	372	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_905203305.1	s__CAG-269 sp905203305	83.1265	234	372	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	-
GCA_900556865.1	s__CAG-269 sp900556865	78.3628	89	372	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	-
GCA_003518755.1	s__CAG-269 sp003518755	77.6566	108	372	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	-
GCA_900554175.1	s__CAG-269 sp900554175	77.5536	105	372	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.99	99.99	0.98	0.96	3	-
GCA_017409455.1	s__CAG-269 sp017409455	77.3367	83	372	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	-
GCA_900553985.1	s__CAG-269 sp900553985	77.2028	108	372	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.48	98.04	0.82	0.80	5	-
GCA_900555615.1	s__CAG-269 sp900555615	77.1607	94	372	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	97.95	97.78	0.76	0.74	3	-
GCA_900556695.1	s__CAG-269 sp900556695	77.131	81	372	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	-
GCA_001916055.1	s__CAG-269 sp001916055	77.0448	104	372	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.37	97.96	0.88	0.86	4	-
GCA_904419495.1	s__CAG-269 sp904419495	76.7266	87	372	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	-
--------------------------------------------------------------------------------
[2023-06-05 18:57:23,300] [INFO] GTDB search result was written to GCA_934167375.1_ERR7738563_bin.172_genomic.fna/result_gtdb.tsv
[2023-06-05 18:57:23,300] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:57:23,303] [INFO] DFAST_QC result json was written to GCA_934167375.1_ERR7738563_bin.172_genomic.fna/dqc_result.json
[2023-06-05 18:57:23,303] [INFO] DFAST_QC completed!
[2023-06-05 18:57:23,303] [INFO] Total running time: 0h0m25s