[2023-06-07 22:34:46,844] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:34:46,845] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:34:46,846] [INFO] DQC Reference Directory: /var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference
[2023-06-07 22:34:48,133] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:34:48,133] [INFO] Task started: Prodigal
[2023-06-07 22:34:48,134] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b4d9674-efba-416a-b48b-1f9f3ff9679d/GCA_902635965.1_AG-916-A19_genomic.fna.gz | prodigal -d GCA_902635965.1_AG-916-A19_genomic.fna/cds.fna -a GCA_902635965.1_AG-916-A19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:34:53,471] [INFO] Task succeeded: Prodigal
[2023-06-07 22:34:53,472] [INFO] Task started: HMMsearch
[2023-06-07 22:34:53,472] [INFO] Running command: hmmsearch --tblout GCA_902635965.1_AG-916-A19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference/reference_markers.hmm GCA_902635965.1_AG-916-A19_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:34:53,724] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:34:53,725] [INFO] Found 6/6 markers.
[2023-06-07 22:34:53,763] [INFO] Query marker FASTA was written to GCA_902635965.1_AG-916-A19_genomic.fna/markers.fasta
[2023-06-07 22:34:53,764] [INFO] Task started: Blastn
[2023-06-07 22:34:53,764] [INFO] Running command: blastn -query GCA_902635965.1_AG-916-A19_genomic.fna/markers.fasta -db /var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference/reference_markers.fasta -out GCA_902635965.1_AG-916-A19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:34:54,403] [INFO] Task succeeded: Blastn
[2023-06-07 22:34:54,408] [INFO] Selected 25 target genomes.
[2023-06-07 22:34:54,408] [INFO] Target genome list was writen to GCA_902635965.1_AG-916-A19_genomic.fna/target_genomes.txt
[2023-06-07 22:34:54,415] [INFO] Task started: fastANI
[2023-06-07 22:34:54,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b4d9674-efba-416a-b48b-1f9f3ff9679d/GCA_902635965.1_AG-916-A19_genomic.fna.gz --refList GCA_902635965.1_AG-916-A19_genomic.fna/target_genomes.txt --output GCA_902635965.1_AG-916-A19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:35:08,234] [INFO] Task succeeded: fastANI
[2023-06-07 22:35:08,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:35:08,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:35:08,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:35:08,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 22:35:08,238] [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
--------------------------------------------------------------------------------
[2023-06-07 22:35:08,240] [INFO] DFAST Taxonomy check result was written to GCA_902635965.1_AG-916-A19_genomic.fna/tc_result.tsv
[2023-06-07 22:35:08,241] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:35:08,241] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:35:08,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference/checkm_data
[2023-06-07 22:35:08,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:35:08,280] [INFO] Task started: CheckM
[2023-06-07 22:35:08,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635965.1_AG-916-A19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635965.1_AG-916-A19_genomic.fna/checkm_input GCA_902635965.1_AG-916-A19_genomic.fna/checkm_result
[2023-06-07 22:35:30,763] [INFO] Task succeeded: CheckM
[2023-06-07 22:35:30,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:35:30,781] [INFO] ===== Completeness check finished =====
[2023-06-07 22:35:30,781] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:35:30,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635965.1_AG-916-A19_genomic.fna/markers.fasta)
[2023-06-07 22:35:30,782] [INFO] Task started: Blastn
[2023-06-07 22:35:30,782] [INFO] Running command: blastn -query GCA_902635965.1_AG-916-A19_genomic.fna/markers.fasta -db /var/lib/cwl/stgef3f87ef-c2fa-402b-9952-28f7b0191b60/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635965.1_AG-916-A19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:35:31,737] [INFO] Task succeeded: Blastn
[2023-06-07 22:35:31,742] [INFO] Selected 9 target genomes.
[2023-06-07 22:35:31,742] [INFO] Target genome list was writen to GCA_902635965.1_AG-916-A19_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:35:31,746] [INFO] Task started: fastANI
[2023-06-07 22:35:31,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b4d9674-efba-416a-b48b-1f9f3ff9679d/GCA_902635965.1_AG-916-A19_genomic.fna.gz --refList GCA_902635965.1_AG-916-A19_genomic.fna/target_genomes_gtdb.txt --output GCA_902635965.1_AG-916-A19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:35:34,869] [INFO] Task succeeded: fastANI
[2023-06-07 22:35:34,885] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:35:34,886] [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_902635965.1	s__TMED96 sp902635965	100.0	563	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	97.75	95.54	0.87	0.85	3	conclusive
GCA_902582405.1	s__TMED96 sp902582405	86.2748	336	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	99.80	99.80	0.73	0.73	2	-
GCA_902595825.1	s__TMED96 sp902595825	86.0159	316	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593075.1	s__TMED96 sp902593075	85.4572	331	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728075.1	s__TMED96 sp002728075	85.3684	362	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902598305.1	s__TMED96 sp902598305	85.2835	469	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171475.2	s__TMED96 sp002171475	84.9688	440	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	99.27	99.27	0.93	0.93	2	-
GCA_902628605.1	s__TMED96 sp902628605	84.5462	211	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167525.1	s__MS024-2A sp002167525	77.9261	50	567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.89	98.89	0.72	0.72	2	-
--------------------------------------------------------------------------------
[2023-06-07 22:35:34,888] [INFO] GTDB search result was written to GCA_902635965.1_AG-916-A19_genomic.fna/result_gtdb.tsv
[2023-06-07 22:35:34,888] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:35:34,892] [INFO] DFAST_QC result json was written to GCA_902635965.1_AG-916-A19_genomic.fna/dqc_result.json
[2023-06-07 22:35:34,892] [INFO] DFAST_QC completed!
[2023-06-07 22:35:34,893] [INFO] Total running time: 0h0m48s