[2023-03-19 01:50:01,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference
[2023-03-19 01:50:03,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,565] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,565] [INFO] Running command: cat /var/lib/cwl/stg8a40651f-c612-47f2-a40d-7de23d2eef74/OceanDNA-b3219.fa | prodigal -d OceanDNA-b3219/cds.fna -a OceanDNA-b3219/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:13,979] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:13,980] [INFO] Task started: HMMsearch
[2023-03-19 01:50:13,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b3219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference/reference_markers.hmm OceanDNA-b3219/protein.faa > /dev/null
[2023-03-19 01:50:14,155] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:14,156] [INFO] Found 6/6 markers.
[2023-03-19 01:50:14,170] [INFO] Query marker FASTA was written to OceanDNA-b3219/markers.fasta
[2023-03-19 01:50:14,171] [INFO] Task started: Blastn
[2023-03-19 01:50:14,172] [INFO] Running command: blastn -query OceanDNA-b3219/markers.fasta -db /var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference/reference_markers.fasta -out OceanDNA-b3219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:14,696] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:14,697] [INFO] Selected 30 target genomes.
[2023-03-19 01:50:14,697] [INFO] Target genome list was writen to OceanDNA-b3219/target_genomes.txt
[2023-03-19 01:50:14,721] [INFO] Task started: fastANI
[2023-03-19 01:50:14,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a40651f-c612-47f2-a40d-7de23d2eef74/OceanDNA-b3219.fa --refList OceanDNA-b3219/target_genomes.txt --output OceanDNA-b3219/fastani_result.tsv --threads 1
[2023-03-19 01:50:34,475] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:34,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:34,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:34,476] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:34,476] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:34,476] [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 01:50:34,480] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3219/tc_result.tsv
[2023-03-19 01:50:34,480] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:34,480] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:34,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference/checkm_data
[2023-03-19 01:50:34,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:34,487] [INFO] Task started: CheckM
[2023-03-19 01:50:34,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3219/checkm_input OceanDNA-b3219/checkm_result
[2023-03-19 01:51:05,020] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:05,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:05,057] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:05,057] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:05,057] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3219/markers.fasta)
[2023-03-19 01:51:05,058] [INFO] Task started: Blastn
[2023-03-19 01:51:05,058] [INFO] Running command: blastn -query OceanDNA-b3219/markers.fasta -db /var/lib/cwl/stg63a70b44-fc61-4c67-809f-89d4d915f759/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:05,774] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:05,775] [INFO] Selected 15 target genomes.
[2023-03-19 01:51:05,775] [INFO] Target genome list was writen to OceanDNA-b3219/target_genomes_gtdb.txt
[2023-03-19 01:51:05,787] [INFO] Task started: fastANI
[2023-03-19 01:51:05,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a40651f-c612-47f2-a40d-7de23d2eef74/OceanDNA-b3219.fa --refList OceanDNA-b3219/target_genomes_gtdb.txt --output OceanDNA-b3219/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:11,940] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:11,945] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:51:11,945] [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_002365735.1	s__UBA4592 sp002365735	99.1772	457	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	97.71	97.71	0.84	0.84	2	conclusive
GCA_905181745.1	s__UBA4592 sp905181745	89.8286	269	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390705.1	s__UBA4592 sp002390705	88.0366	456	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	99.34	99.13	0.94	0.92	9	-
GCA_002469525.1	s__UBA4592 sp002469525	78.3949	119	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	99.66	99.57	0.88	0.85	6	-
GCA_017854795.1	s__UBA4592 sp017854795	78.1237	162	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	99.75	99.75	0.97	0.97	2	-
GCA_017857175.1	s__UBA6154 sp017857175	77.348	51	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	99.75	99.69	0.94	0.93	4	-
GCA_017857705.1	s__UBA4592 sp017857705	77.2238	123	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:11,947] [INFO] GTDB search result was written to OceanDNA-b3219/result_gtdb.tsv
[2023-03-19 01:51:11,950] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:11,951] [INFO] DFAST_QC result json was written to OceanDNA-b3219/dqc_result.json
[2023-03-19 01:51:11,951] [INFO] DFAST_QC completed!
[2023-03-19 01:51:11,951] [INFO] Total running time: 0h1m10s