[2023-03-19 03:14:58,239] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:14:58,239] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:14:58,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference
[2023-03-19 03:14:59,373] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:14:59,374] [INFO] Task started: Prodigal
[2023-03-19 03:14:59,374] [INFO] Running command: cat /var/lib/cwl/stg5f433d84-c631-47d9-928c-b0b923f452d9/OceanDNA-b9565.fa | prodigal -d OceanDNA-b9565/cds.fna -a OceanDNA-b9565/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:15:12,653] [INFO] Task succeeded: Prodigal
[2023-03-19 03:15:12,654] [INFO] Task started: HMMsearch
[2023-03-19 03:15:12,654] [INFO] Running command: hmmsearch --tblout OceanDNA-b9565/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference/reference_markers.hmm OceanDNA-b9565/protein.faa > /dev/null
[2023-03-19 03:15:12,834] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:15:12,834] [INFO] Found 6/6 markers.
[2023-03-19 03:15:12,847] [INFO] Query marker FASTA was written to OceanDNA-b9565/markers.fasta
[2023-03-19 03:15:12,848] [INFO] Task started: Blastn
[2023-03-19 03:15:12,848] [INFO] Running command: blastn -query OceanDNA-b9565/markers.fasta -db /var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference/reference_markers.fasta -out OceanDNA-b9565/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:15:13,376] [INFO] Task succeeded: Blastn
[2023-03-19 03:15:13,377] [INFO] Selected 29 target genomes.
[2023-03-19 03:15:13,377] [INFO] Target genome list was writen to OceanDNA-b9565/target_genomes.txt
[2023-03-19 03:15:13,396] [INFO] Task started: fastANI
[2023-03-19 03:15:13,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f433d84-c631-47d9-928c-b0b923f452d9/OceanDNA-b9565.fa --refList OceanDNA-b9565/target_genomes.txt --output OceanDNA-b9565/fastani_result.tsv --threads 1
[2023-03-19 03:15:28,255] [INFO] Task succeeded: fastANI
[2023-03-19 03:15:28,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:15:28,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:15:28,255] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:15:28,255] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:15:28,256] [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
--------------------------------------------------------------------------------
[2023-03-19 03:15:28,256] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9565/tc_result.tsv
[2023-03-19 03:15:28,256] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:15:28,256] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:15:28,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference/checkm_data
[2023-03-19 03:15:28,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:15:28,262] [INFO] Task started: CheckM
[2023-03-19 03:15:28,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9565/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9565/checkm_input OceanDNA-b9565/checkm_result
[2023-03-19 03:16:05,220] [INFO] Task succeeded: CheckM
[2023-03-19 03:16:05,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:16:05,234] [INFO] ===== Completeness check finished =====
[2023-03-19 03:16:05,234] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:16:05,234] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9565/markers.fasta)
[2023-03-19 03:16:05,235] [INFO] Task started: Blastn
[2023-03-19 03:16:05,235] [INFO] Running command: blastn -query OceanDNA-b9565/markers.fasta -db /var/lib/cwl/stg1de3eb2e-d8d6-48c9-87da-9cc277aa5736/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9565/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:16:05,973] [INFO] Task succeeded: Blastn
[2023-03-19 03:16:05,974] [INFO] Selected 21 target genomes.
[2023-03-19 03:16:05,974] [INFO] Target genome list was writen to OceanDNA-b9565/target_genomes_gtdb.txt
[2023-03-19 03:16:06,058] [INFO] Task started: fastANI
[2023-03-19 03:16:06,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f433d84-c631-47d9-928c-b0b923f452d9/OceanDNA-b9565.fa --refList OceanDNA-b9565/target_genomes_gtdb.txt --output OceanDNA-b9565/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:16:13,093] [INFO] Task succeeded: fastANI
[2023-03-19 03:16:13,101] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:16:13,101] [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_002292265.1	s__MS024-2A sp002292265	99.8715	575	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	conclusive
GCA_017852075.1	s__MS024-2A sp017852075	80.5474	418	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_008081175.1	s__MS024-2A sp008081175	77.8507	121	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.02	98.61	0.90	0.80	6	-
GCA_002705385.1	s__MS024-2A sp002705385	77.7109	68	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	77.6807	121	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_002167945.1	s__MS024-2A sp002167945	77.2898	116	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714815.1	s__MS024-2A sp002714815	77.0207	131	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	76.9409	89	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181895.1	s__MS024-2A sp905181895	76.8025	62	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606525.1	s__MS024-2A sp902606525	76.7546	65	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	76.4704	73	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023645.1	s__UBA7428 sp003023645	75.9061	50	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_011526365.1	s__RFYP01 sp011526365	75.6853	56	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RFYP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:16:13,101] [INFO] GTDB search result was written to OceanDNA-b9565/result_gtdb.tsv
[2023-03-19 03:16:13,102] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:16:13,103] [INFO] DFAST_QC result json was written to OceanDNA-b9565/dqc_result.json
[2023-03-19 03:16:13,103] [INFO] DFAST_QC completed!
[2023-03-19 03:16:13,103] [INFO] Total running time: 0h1m15s