[2023-03-17 04:15:14,701] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,701] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,701] [INFO] DQC Reference Directory: /var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference
[2023-03-17 04:15:16,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,099] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,099] [INFO] Running command: cat /var/lib/cwl/stgdc2e9215-04c3-454a-9c21-9787a9abc91c/OceanDNA-b3150.fa | prodigal -d OceanDNA-b3150/cds.fna -a OceanDNA-b3150/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:27,239] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:27,239] [INFO] Task started: HMMsearch
[2023-03-17 04:15:27,239] [INFO] Running command: hmmsearch --tblout OceanDNA-b3150/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference/reference_markers.hmm OceanDNA-b3150/protein.faa > /dev/null
[2023-03-17 04:15:27,420] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:27,420] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdc2e9215-04c3-454a-9c21-9787a9abc91c/OceanDNA-b3150.fa]
[2023-03-17 04:15:27,434] [INFO] Query marker FASTA was written to OceanDNA-b3150/markers.fasta
[2023-03-17 04:15:27,435] [INFO] Task started: Blastn
[2023-03-17 04:15:27,435] [INFO] Running command: blastn -query OceanDNA-b3150/markers.fasta -db /var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference/reference_markers.fasta -out OceanDNA-b3150/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:28,077] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:28,078] [INFO] Selected 30 target genomes.
[2023-03-17 04:15:28,079] [INFO] Target genome list was writen to OceanDNA-b3150/target_genomes.txt
[2023-03-17 04:15:28,094] [INFO] Task started: fastANI
[2023-03-17 04:15:28,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc2e9215-04c3-454a-9c21-9787a9abc91c/OceanDNA-b3150.fa --refList OceanDNA-b3150/target_genomes.txt --output OceanDNA-b3150/fastani_result.tsv --threads 1
[2023-03-17 04:15:51,254] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:51,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:51,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:51,258] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:51,258] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:51,258] [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
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	76.2017	52	572	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	75.9133	51	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:51,258] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3150/tc_result.tsv
[2023-03-17 04:15:51,258] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:51,258] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:51,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference/checkm_data
[2023-03-17 04:15:51,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:51,265] [INFO] Task started: CheckM
[2023-03-17 04:15:51,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3150/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3150/checkm_input OceanDNA-b3150/checkm_result
[2023-03-17 04:16:22,703] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:22,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:22,706] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:22,706] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:22,706] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3150/markers.fasta)
[2023-03-17 04:16:22,706] [INFO] Task started: Blastn
[2023-03-17 04:16:22,706] [INFO] Running command: blastn -query OceanDNA-b3150/markers.fasta -db /var/lib/cwl/stgc12bec1e-ac70-4c58-9971-71af4cb5a16e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3150/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:23,742] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:23,742] [INFO] Selected 18 target genomes.
[2023-03-17 04:16:23,743] [INFO] Target genome list was writen to OceanDNA-b3150/target_genomes_gtdb.txt
[2023-03-17 04:16:24,086] [INFO] Task started: fastANI
[2023-03-17 04:16:24,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc2e9215-04c3-454a-9c21-9787a9abc91c/OceanDNA-b3150.fa --refList OceanDNA-b3150/target_genomes_gtdb.txt --output OceanDNA-b3150/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:31,891] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:31,898] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:31,898] [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_018402235.1	s__S36-B12 sp018402235	78.414	213	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728915.1	s__S36-B12 sp002728915	78.1319	115	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	99.13	98.99	0.85	0.80	4	-
GCA_012103605.1	s__S36-B12 sp012103605	78.1292	111	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	95.57	95.57	0.76	0.76	2	-
GCA_002694095.1	s__S36-B12 sp002694095	78.0701	104	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	97.65	97.49	0.82	0.80	3	-
GCA_002729215.1	s__S36-B12 sp002729215	77.9629	117	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.32	97.43	0.87	0.81	12	-
GCA_010029945.1	s__S36-B12 sp010029945	77.865	113	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.25	98.18	0.79	0.75	5	-
GCA_903934925.1	s__UBA10649 sp903934925	76.7122	70	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	99.42	99.35	0.85	0.83	4	-
GCA_903908025.1	s__UBA10649 sp903908025	76.6907	62	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.87	97.91	0.84	0.77	3	-
GCA_016870195.1	s__VGCC01 sp016870195	76.6623	79	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__VGCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699015.1	s__WLND01 sp009699015	76.3316	68	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
GCA_017849335.1	s__UBA10649 sp017849335	76.2144	65	572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:31,899] [INFO] GTDB search result was written to OceanDNA-b3150/result_gtdb.tsv
[2023-03-17 04:16:31,899] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:31,900] [INFO] DFAST_QC result json was written to OceanDNA-b3150/dqc_result.json
[2023-03-17 04:16:31,900] [INFO] DFAST_QC completed!
[2023-03-17 04:16:31,900] [INFO] Total running time: 0h1m17s