[2023-06-28 06:48:27,065] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:48:27,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:48:27,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference
[2023-06-28 06:48:28,313] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:48:28,314] [INFO] Task started: Prodigal
[2023-06-28 06:48:28,314] [INFO] Running command: gunzip -c /var/lib/cwl/stg4efd0a86-9b22-4d52-9041-82464e91f2cf/GCA_944384235.1_E0_LS_bin164_genomic.fna.gz | prodigal -d GCA_944384235.1_E0_LS_bin164_genomic.fna/cds.fna -a GCA_944384235.1_E0_LS_bin164_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:48:31,536] [INFO] Task succeeded: Prodigal
[2023-06-28 06:48:31,536] [INFO] Task started: HMMsearch
[2023-06-28 06:48:31,536] [INFO] Running command: hmmsearch --tblout GCA_944384235.1_E0_LS_bin164_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference/reference_markers.hmm GCA_944384235.1_E0_LS_bin164_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:48:31,781] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:48:31,782] [INFO] Found 6/6 markers.
[2023-06-28 06:48:31,805] [INFO] Query marker FASTA was written to GCA_944384235.1_E0_LS_bin164_genomic.fna/markers.fasta
[2023-06-28 06:48:31,806] [INFO] Task started: Blastn
[2023-06-28 06:48:31,806] [INFO] Running command: blastn -query GCA_944384235.1_E0_LS_bin164_genomic.fna/markers.fasta -db /var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference/reference_markers.fasta -out GCA_944384235.1_E0_LS_bin164_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:48:32,423] [INFO] Task succeeded: Blastn
[2023-06-28 06:48:32,430] [INFO] Selected 20 target genomes.
[2023-06-28 06:48:32,430] [INFO] Target genome list was writen to GCA_944384235.1_E0_LS_bin164_genomic.fna/target_genomes.txt
[2023-06-28 06:48:32,433] [INFO] Task started: fastANI
[2023-06-28 06:48:32,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efd0a86-9b22-4d52-9041-82464e91f2cf/GCA_944384235.1_E0_LS_bin164_genomic.fna.gz --refList GCA_944384235.1_E0_LS_bin164_genomic.fna/target_genomes.txt --output GCA_944384235.1_E0_LS_bin164_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:48:40,985] [INFO] Task succeeded: fastANI
[2023-06-28 06:48:40,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:48:40,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:48:40,995] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:48:40,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:48:40,996] [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
[Clostridium] colinum	strain=DSM 6011	GCA_940677205.1	36835	36835	type	True	75.9595	62	569	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:48:40,998] [INFO] DFAST Taxonomy check result was written to GCA_944384235.1_E0_LS_bin164_genomic.fna/tc_result.tsv
[2023-06-28 06:48:40,999] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:48:41,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:48:41,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference/checkm_data
[2023-06-28 06:48:41,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:48:41,027] [INFO] Task started: CheckM
[2023-06-28 06:48:41,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384235.1_E0_LS_bin164_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384235.1_E0_LS_bin164_genomic.fna/checkm_input GCA_944384235.1_E0_LS_bin164_genomic.fna/checkm_result
[2023-06-28 06:48:59,228] [INFO] Task succeeded: CheckM
[2023-06-28 06:48:59,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:48:59,246] [INFO] ===== Completeness check finished =====
[2023-06-28 06:48:59,246] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:48:59,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384235.1_E0_LS_bin164_genomic.fna/markers.fasta)
[2023-06-28 06:48:59,247] [INFO] Task started: Blastn
[2023-06-28 06:48:59,247] [INFO] Running command: blastn -query GCA_944384235.1_E0_LS_bin164_genomic.fna/markers.fasta -db /var/lib/cwl/stg2313c25d-a64f-4d0a-9da7-3bac4059b438/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384235.1_E0_LS_bin164_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:49:00,300] [INFO] Task succeeded: Blastn
[2023-06-28 06:49:00,305] [INFO] Selected 26 target genomes.
[2023-06-28 06:49:00,305] [INFO] Target genome list was writen to GCA_944384235.1_E0_LS_bin164_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:49:00,322] [INFO] Task started: fastANI
[2023-06-28 06:49:00,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efd0a86-9b22-4d52-9041-82464e91f2cf/GCA_944384235.1_E0_LS_bin164_genomic.fna.gz --refList GCA_944384235.1_E0_LS_bin164_genomic.fna/target_genomes_gtdb.txt --output GCA_944384235.1_E0_LS_bin164_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:49:09,918] [INFO] Task succeeded: fastANI
[2023-06-28 06:49:09,933] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 06:49:09,934] [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_900543365.1	s__Gallispira sp900543365	78.8963	176	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	99.75	99.35	0.91	0.83	4	-
GCA_900551755.1	s__Gallispira sp900551755	78.7778	179	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	99.95	99.95	0.89	0.89	2	-
GCA_905201505.1	s__Gallispira sp905201505	78.5943	169	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904395805.1	s__Gallispira edinburgensis	78.2813	133	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760465.1	s__HGM11788 sp900760465	77.929	89	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__HGM11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432155.1	s__CAG-274 sp000432155	77.8349	106	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__CAG-274	95.0	98.95	98.88	0.91	0.89	4	-
GCA_900545305.1	s__CAG-274 sp900545305	77.2429	114	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__CAG-274	95.0	98.57	98.54	0.89	0.87	5	-
GCA_018371275.1	s__JAHALF01 sp018371275	76.2194	56	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__JAHALF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:49:09,936] [INFO] GTDB search result was written to GCA_944384235.1_E0_LS_bin164_genomic.fna/result_gtdb.tsv
[2023-06-28 06:49:09,936] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:49:09,939] [INFO] DFAST_QC result json was written to GCA_944384235.1_E0_LS_bin164_genomic.fna/dqc_result.json
[2023-06-28 06:49:09,939] [INFO] DFAST_QC completed!
[2023-06-28 06:49:09,939] [INFO] Total running time: 0h0m43s