[2023-03-18 02:14:52,677] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:14:52,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:14:52,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference
[2023-03-18 02:14:53,776] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:14:53,776] [INFO] Task started: Prodigal
[2023-03-18 02:14:53,777] [INFO] Running command: cat /var/lib/cwl/stg5a8fe933-b795-469a-9881-e36bb9c31729/OceanDNA-b24489.fa | prodigal -d OceanDNA-b24489/cds.fna -a OceanDNA-b24489/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:14:58,946] [INFO] Task succeeded: Prodigal
[2023-03-18 02:14:58,947] [INFO] Task started: HMMsearch
[2023-03-18 02:14:58,947] [INFO] Running command: hmmsearch --tblout OceanDNA-b24489/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference/reference_markers.hmm OceanDNA-b24489/protein.faa > /dev/null
[2023-03-18 02:14:59,093] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:14:59,094] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a8fe933-b795-469a-9881-e36bb9c31729/OceanDNA-b24489.fa]
[2023-03-18 02:14:59,122] [INFO] Query marker FASTA was written to OceanDNA-b24489/markers.fasta
[2023-03-18 02:14:59,124] [INFO] Task started: Blastn
[2023-03-18 02:14:59,124] [INFO] Running command: blastn -query OceanDNA-b24489/markers.fasta -db /var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference/reference_markers.fasta -out OceanDNA-b24489/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:14:59,706] [INFO] Task succeeded: Blastn
[2023-03-18 02:14:59,707] [INFO] Selected 17 target genomes.
[2023-03-18 02:14:59,707] [INFO] Target genome list was writen to OceanDNA-b24489/target_genomes.txt
[2023-03-18 02:14:59,718] [INFO] Task started: fastANI
[2023-03-18 02:14:59,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8fe933-b795-469a-9881-e36bb9c31729/OceanDNA-b24489.fa --refList OceanDNA-b24489/target_genomes.txt --output OceanDNA-b24489/fastani_result.tsv --threads 1
[2023-03-18 02:15:05,795] [INFO] Task succeeded: fastANI
[2023-03-18 02:15:05,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:15:05,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:15:05,796] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:15:05,796] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:15:05,796] [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 02:15:05,796] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24489/tc_result.tsv
[2023-03-18 02:15:05,796] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:15:05,796] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:15:05,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference/checkm_data
[2023-03-18 02:15:05,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:15:05,835] [INFO] Task started: CheckM
[2023-03-18 02:15:05,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24489/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24489/checkm_input OceanDNA-b24489/checkm_result
[2023-03-18 02:15:25,468] [INFO] Task succeeded: CheckM
[2023-03-18 02:15:25,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.58%
Contamintation: 3.07%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:15:25,504] [INFO] ===== Completeness check finished =====
[2023-03-18 02:15:25,504] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:15:25,504] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24489/markers.fasta)
[2023-03-18 02:15:25,505] [INFO] Task started: Blastn
[2023-03-18 02:15:25,505] [INFO] Running command: blastn -query OceanDNA-b24489/markers.fasta -db /var/lib/cwl/stg7d35ccd2-04c0-412f-b0ed-92fd28651f7a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24489/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:15:26,272] [INFO] Task succeeded: Blastn
[2023-03-18 02:15:26,273] [INFO] Selected 18 target genomes.
[2023-03-18 02:15:26,273] [INFO] Target genome list was writen to OceanDNA-b24489/target_genomes_gtdb.txt
[2023-03-18 02:15:26,299] [INFO] Task started: fastANI
[2023-03-18 02:15:26,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8fe933-b795-469a-9881-e36bb9c31729/OceanDNA-b24489.fa --refList OceanDNA-b24489/target_genomes_gtdb.txt --output OceanDNA-b24489/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:15:29,978] [INFO] Task succeeded: fastANI
[2023-03-18 02:15:29,987] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:15:29,988] [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_000299115.1	s__HIMB59 sp000299115	91.5409	217	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529795.1	s__HIMB59 sp902529795	88.0601	145	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522585.1	s__HIMB59 sp902522585	85.7322	123	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638215.1	s__HIMB59 sp008638215	83.921	172	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.46	99.38	0.89	0.85	4	-
GCA_004321805.1	s__HIMB59 sp004321805	79.7458	118	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509695.1	s__HIMB59 sp902509695	78.2992	78	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515765.1	s__HIMB59 sp902515765	78.1838	77	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546975.1	s__HIMB59 sp902546975	78.0675	90	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.15	95.57	0.84	0.81	5	-
GCA_002169365.1	s__HIMB59 sp002169365	77.9327	63	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616855.1	s__HIMB59 sp902616855	77.7716	75	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.19	95.15	0.77	0.74	3	-
GCA_902591315.1	s__HIMB59 sp902591315	77.725	63	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.30	0.78	0.78	2	-
GCA_902613185.1	s__HIMB59 sp902613185	77.6113	103	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.61	99.58	0.93	0.92	5	-
GCA_902611415.1	s__HIMB59 sp902611415	77.3174	82	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902527545.1	s__HIMB59 sp902527545	77.2392	84	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.61	99.43	0.88	0.87	4	-
GCA_902601865.1	s__HIMB59 sp902601865	77.1974	91	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521795.1	s__HIMB59 sp902560595	77.0038	85	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.49	95.27	0.76	0.73	4	-
--------------------------------------------------------------------------------
[2023-03-18 02:15:29,988] [INFO] GTDB search result was written to OceanDNA-b24489/result_gtdb.tsv
[2023-03-18 02:15:29,988] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:15:29,989] [INFO] DFAST_QC result json was written to OceanDNA-b24489/dqc_result.json
[2023-03-18 02:15:29,989] [INFO] DFAST_QC completed!
[2023-03-18 02:15:29,989] [INFO] Total running time: 0h0m37s