[2023-06-04 21:24:57,698] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:24:57,700] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:24:57,700] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference
[2023-06-04 21:24:59,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:24:59,071] [INFO] Task started: Prodigal
[2023-06-04 21:24:59,072] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9b2d468-30a6-4ed5-a9be-4a8b28f6db39/GCA_934149335.1_ERR7745743_bin.274_genomic.fna.gz | prodigal -d GCA_934149335.1_ERR7745743_bin.274_genomic.fna/cds.fna -a GCA_934149335.1_ERR7745743_bin.274_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:25:01,270] [INFO] Task succeeded: Prodigal
[2023-06-04 21:25:01,270] [INFO] Task started: HMMsearch
[2023-06-04 21:25:01,271] [INFO] Running command: hmmsearch --tblout GCA_934149335.1_ERR7745743_bin.274_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference/reference_markers.hmm GCA_934149335.1_ERR7745743_bin.274_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:25:01,541] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:25:01,542] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9b2d468-30a6-4ed5-a9be-4a8b28f6db39/GCA_934149335.1_ERR7745743_bin.274_genomic.fna.gz]
[2023-06-04 21:25:01,563] [INFO] Query marker FASTA was written to GCA_934149335.1_ERR7745743_bin.274_genomic.fna/markers.fasta
[2023-06-04 21:25:01,564] [INFO] Task started: Blastn
[2023-06-04 21:25:01,564] [INFO] Running command: blastn -query GCA_934149335.1_ERR7745743_bin.274_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference/reference_markers.fasta -out GCA_934149335.1_ERR7745743_bin.274_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:02,251] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:02,254] [INFO] Selected 24 target genomes.
[2023-06-04 21:25:02,255] [INFO] Target genome list was writen to GCA_934149335.1_ERR7745743_bin.274_genomic.fna/target_genomes.txt
[2023-06-04 21:25:02,289] [INFO] Task started: fastANI
[2023-06-04 21:25:02,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b2d468-30a6-4ed5-a9be-4a8b28f6db39/GCA_934149335.1_ERR7745743_bin.274_genomic.fna.gz --refList GCA_934149335.1_ERR7745743_bin.274_genomic.fna/target_genomes.txt --output GCA_934149335.1_ERR7745743_bin.274_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:25:13,920] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:13,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:25:13,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:25:13,922] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:25:13,923] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:25:13,923] [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
--------------------------------------------------------------------------------
[2023-06-04 21:25:13,930] [INFO] DFAST Taxonomy check result was written to GCA_934149335.1_ERR7745743_bin.274_genomic.fna/tc_result.tsv
[2023-06-04 21:25:13,931] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:25:13,931] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:25:13,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference/checkm_data
[2023-06-04 21:25:13,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:25:13,955] [INFO] Task started: CheckM
[2023-06-04 21:25:13,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934149335.1_ERR7745743_bin.274_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934149335.1_ERR7745743_bin.274_genomic.fna/checkm_input GCA_934149335.1_ERR7745743_bin.274_genomic.fna/checkm_result
[2023-06-04 21:25:30,051] [INFO] Task succeeded: CheckM
[2023-06-04 21:25:30,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:25:30,080] [INFO] ===== Completeness check finished =====
[2023-06-04 21:25:30,082] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:25:30,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934149335.1_ERR7745743_bin.274_genomic.fna/markers.fasta)
[2023-06-04 21:25:30,083] [INFO] Task started: Blastn
[2023-06-04 21:25:30,083] [INFO] Running command: blastn -query GCA_934149335.1_ERR7745743_bin.274_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2401765-6953-42de-b5e9-0c43452cbdf8/dqc_reference/reference_markers_gtdb.fasta -out GCA_934149335.1_ERR7745743_bin.274_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:30,958] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:30,966] [INFO] Selected 18 target genomes.
[2023-06-04 21:25:30,966] [INFO] Target genome list was writen to GCA_934149335.1_ERR7745743_bin.274_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:25:30,975] [INFO] Task started: fastANI
[2023-06-04 21:25:30,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b2d468-30a6-4ed5-a9be-4a8b28f6db39/GCA_934149335.1_ERR7745743_bin.274_genomic.fna.gz --refList GCA_934149335.1_ERR7745743_bin.274_genomic.fna/target_genomes_gtdb.txt --output GCA_934149335.1_ERR7745743_bin.274_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:25:35,433] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:35,454] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 21:25:35,454] [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_900543055.1	s__UBA3789 sp900543055	83.2113	289	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.54	97.21	0.78	0.56	4	-
GCA_902776735.1	s__UBA3789 sp902776735	79.5534	174	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.25	98.05	0.74	0.72	3	-
GCA_900314225.1	s__UBA3789 sp900314225	79.3418	163	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.63	98.32	0.75	0.71	4	-
GCA_002369415.1	s__UBA3789 sp002369415	79.2757	172	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433415.1	s__UBA3789 sp017433415	78.8802	136	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780585.1	s__UBA3789 sp902780585	78.8619	137	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.24	98.24	0.79	0.79	2	-
GCA_000432835.1	s__CAG-417 sp000432835	78.6809	77	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	98.45	98.23	0.92	0.90	4	-
GCA_910589335.1	s__UBA3789 sp910589335	78.6555	170	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768065.1	s__UBA3789 sp902768065	78.6552	172	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622175.1	s__CAG-877 sp017622175	78.5803	136	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780395.1	s__UBA3789 sp902780395	78.5092	151	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783435.1	s__UBA3789 sp902783435	78.3902	171	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293205.1	s__CAG-877 sp016293205	78.3852	138	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796215.1	s__UBA3789 sp902796215	78.032	110	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320505.1	s__UBA2730 sp900320505	76.877	58	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA2730	95.0	99.47	98.93	0.92	0.85	3	-
GCA_900319955.1	s__UBA2730 sp900319955	76.6769	52	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA2730	95.0	99.47	99.47	0.88	0.88	2	-
GCA_900313345.1	s__UBA2730 sp900313345	76.3339	53	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA2730	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-04 21:25:35,456] [INFO] GTDB search result was written to GCA_934149335.1_ERR7745743_bin.274_genomic.fna/result_gtdb.tsv
[2023-06-04 21:25:35,457] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:25:35,461] [INFO] DFAST_QC result json was written to GCA_934149335.1_ERR7745743_bin.274_genomic.fna/dqc_result.json
[2023-06-04 21:25:35,461] [INFO] DFAST_QC completed!
[2023-06-04 21:25:35,461] [INFO] Total running time: 0h0m38s