[2023-06-08 09:54:00,160] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:54:00,165] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:54:00,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference
[2023-06-08 09:54:01,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:54:01,656] [INFO] Task started: Prodigal
[2023-06-08 09:54:01,656] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6f337b6-75ad-42ab-8f60-6bb331dea5e2/GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna.gz | prodigal -d GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/cds.fna -a GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:54:12,912] [INFO] Task succeeded: Prodigal
[2023-06-08 09:54:12,912] [INFO] Task started: HMMsearch
[2023-06-08 09:54:12,912] [INFO] Running command: hmmsearch --tblout GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference/reference_markers.hmm GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:54:13,143] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:54:13,144] [INFO] Found 6/6 markers.
[2023-06-08 09:54:13,171] [INFO] Query marker FASTA was written to GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/markers.fasta
[2023-06-08 09:54:13,171] [INFO] Task started: Blastn
[2023-06-08 09:54:13,171] [INFO] Running command: blastn -query GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference/reference_markers.fasta -out GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:13,741] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:13,744] [INFO] Selected 27 target genomes.
[2023-06-08 09:54:13,745] [INFO] Target genome list was writen to GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-08 09:54:13,750] [INFO] Task started: fastANI
[2023-06-08 09:54:13,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f337b6-75ad-42ab-8f60-6bb331dea5e2/GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna.gz --refList GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:54:29,282] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:29,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:54:29,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:54:29,285] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:54:29,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:54:29,285] [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
--------------------------------------------------------------------------------
[2023-06-08 09:54:29,287] [INFO] DFAST Taxonomy check result was written to GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-08 09:54:29,288] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:54:29,288] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:54:29,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference/checkm_data
[2023-06-08 09:54:29,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:54:29,323] [INFO] Task started: CheckM
[2023-06-08 09:54:29,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/checkm_input GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/checkm_result
[2023-06-08 09:55:07,551] [INFO] Task succeeded: CheckM
[2023-06-08 09:55:07,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:55:07,573] [INFO] ===== Completeness check finished =====
[2023-06-08 09:55:07,573] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:55:07,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/markers.fasta)
[2023-06-08 09:55:07,574] [INFO] Task started: Blastn
[2023-06-08 09:55:07,574] [INFO] Running command: blastn -query GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg5589a6b3-3c2d-4204-8518-39e03016a7a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:55:08,313] [INFO] Task succeeded: Blastn
[2023-06-08 09:55:08,318] [INFO] Selected 16 target genomes.
[2023-06-08 09:55:08,318] [INFO] Target genome list was writen to GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:55:08,332] [INFO] Task started: fastANI
[2023-06-08 09:55:08,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f337b6-75ad-42ab-8f60-6bb331dea5e2/GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna.gz --refList GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:55:15,508] [INFO] Task succeeded: fastANI
[2023-06-08 09:55:15,519] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:55:15,520] [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_905480095.1	s__UBA974 sp905480095	88.8621	523	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700285.1	s__UBA974 sp002700285	88.1112	609	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.89	99.89	0.95	0.95	2	-
GCA_002336655.1	s__UBA974 sp002336655	88.0862	474	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663855.1	s__UBA974 sp012963975	77.7117	114	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.32	99.24	0.89	0.87	4	-
GCA_018700255.1	s__UBA974 sp018700255	77.6458	106	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339135.1	s__UBA974 sp002339135	77.567	101	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746975.1	s__UBA974 sp002746975	77.3768	124	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:55:15,522] [INFO] GTDB search result was written to GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 09:55:15,522] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:55:15,526] [INFO] DFAST_QC result json was written to GCA_902752785.1_P4201_102_bin155_mag_fasta_genomic.fna/dqc_result.json
[2023-06-08 09:55:15,527] [INFO] DFAST_QC completed!
[2023-06-08 09:55:15,527] [INFO] Total running time: 0h1m15s