[2023-03-18 05:12:22,308] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:12:22,311] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:12:22,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference
[2023-03-18 05:12:23,420] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:12:23,421] [INFO] Task started: Prodigal
[2023-03-18 05:12:23,421] [INFO] Running command: cat /var/lib/cwl/stg07a40f5a-18b6-4e91-8339-126c9dc34f0b/OceanDNA-b12459.fa | prodigal -d OceanDNA-b12459/cds.fna -a OceanDNA-b12459/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:12:32,732] [INFO] Task succeeded: Prodigal
[2023-03-18 05:12:32,732] [INFO] Task started: HMMsearch
[2023-03-18 05:12:32,732] [INFO] Running command: hmmsearch --tblout OceanDNA-b12459/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference/reference_markers.hmm OceanDNA-b12459/protein.faa > /dev/null
[2023-03-18 05:12:32,926] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:12:32,927] [INFO] Found 6/6 markers.
[2023-03-18 05:12:32,941] [INFO] Query marker FASTA was written to OceanDNA-b12459/markers.fasta
[2023-03-18 05:12:32,942] [INFO] Task started: Blastn
[2023-03-18 05:12:32,943] [INFO] Running command: blastn -query OceanDNA-b12459/markers.fasta -db /var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference/reference_markers.fasta -out OceanDNA-b12459/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:12:33,515] [INFO] Task succeeded: Blastn
[2023-03-18 05:12:33,516] [INFO] Selected 25 target genomes.
[2023-03-18 05:12:33,517] [INFO] Target genome list was writen to OceanDNA-b12459/target_genomes.txt
[2023-03-18 05:12:33,525] [INFO] Task started: fastANI
[2023-03-18 05:12:33,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a40f5a-18b6-4e91-8339-126c9dc34f0b/OceanDNA-b12459.fa --refList OceanDNA-b12459/target_genomes.txt --output OceanDNA-b12459/fastani_result.tsv --threads 1
[2023-03-18 05:12:47,384] [INFO] Task succeeded: fastANI
[2023-03-18 05:12:47,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:12:47,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:12:47,385] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:12:47,385] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:12:47,385] [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
--------------------------------------------------------------------------------
[2023-03-18 05:12:47,390] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12459/tc_result.tsv
[2023-03-18 05:12:47,391] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:12:47,391] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:12:47,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference/checkm_data
[2023-03-18 05:12:47,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:12:47,455] [INFO] Task started: CheckM
[2023-03-18 05:12:47,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12459/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12459/checkm_input OceanDNA-b12459/checkm_result
[2023-03-18 05:13:16,358] [INFO] Task succeeded: CheckM
[2023-03-18 05:13:16,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:13:16,504] [INFO] ===== Completeness check finished =====
[2023-03-18 05:13:16,504] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:13:16,504] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12459/markers.fasta)
[2023-03-18 05:13:16,506] [INFO] Task started: Blastn
[2023-03-18 05:13:16,506] [INFO] Running command: blastn -query OceanDNA-b12459/markers.fasta -db /var/lib/cwl/stg1b71861f-d20e-4f86-adf0-661da717d900/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12459/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:13:17,378] [INFO] Task succeeded: Blastn
[2023-03-18 05:13:17,379] [INFO] Selected 13 target genomes.
[2023-03-18 05:13:17,380] [INFO] Target genome list was writen to OceanDNA-b12459/target_genomes_gtdb.txt
[2023-03-18 05:13:17,393] [INFO] Task started: fastANI
[2023-03-18 05:13:17,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a40f5a-18b6-4e91-8339-126c9dc34f0b/OceanDNA-b12459.fa --refList OceanDNA-b12459/target_genomes_gtdb.txt --output OceanDNA-b12459/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:13:21,573] [INFO] Task succeeded: fastANI
[2023-03-18 05:13:21,580] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:13:21,580] [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_016780365.1	s__MED-G20 sp016780365	98.2064	358	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	conclusive
GCA_905182745.1	s__MED-G20 sp905182745	92.9389	246	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713405.1	s__MED-G20 sp002713405	90.0159	366	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181675.1	s__MED-G20 sp905181675	83.7655	315	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182525.1	s__MED-G20 sp905182525	79.1757	231	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002457645.1	s__MED-G20 sp002457645	78.8454	126	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686655.1	s__MED-G20 sp002686655	78.2659	212	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002691605.1	s__MED-G20 sp002691605	78.2219	178	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_002721285.1	s__SP287 sp002721285	76.8534	56	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536695.1	s__GCA-002727735 sp902536695	76.5473	50	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	97.41	97.41	0.52	0.52	2	-
--------------------------------------------------------------------------------
[2023-03-18 05:13:21,580] [INFO] GTDB search result was written to OceanDNA-b12459/result_gtdb.tsv
[2023-03-18 05:13:21,581] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:13:21,590] [INFO] DFAST_QC result json was written to OceanDNA-b12459/dqc_result.json
[2023-03-18 05:13:21,590] [INFO] DFAST_QC completed!
[2023-03-18 05:13:21,590] [INFO] Total running time: 0h0m59s