[2023-03-17 00:45:47,172] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,172] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg967511be-ba25-4a53-8afa-987d2e98a842/OceanDNA-b45620.fa | prodigal -d OceanDNA-b45620/cds.fna -a OceanDNA-b45620/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:07,334] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:07,334] [INFO] Task started: HMMsearch
[2023-03-17 00:46:07,334] [INFO] Running command: hmmsearch --tblout OceanDNA-b45620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference/reference_markers.hmm OceanDNA-b45620/protein.faa > /dev/null
[2023-03-17 00:46:07,515] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:07,516] [INFO] Found 6/6 markers.
[2023-03-17 00:46:07,531] [INFO] Query marker FASTA was written to OceanDNA-b45620/markers.fasta
[2023-03-17 00:46:07,531] [INFO] Task started: Blastn
[2023-03-17 00:46:07,531] [INFO] Running command: blastn -query OceanDNA-b45620/markers.fasta -db /var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference/reference_markers.fasta -out OceanDNA-b45620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:08,082] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:08,082] [INFO] Selected 10 target genomes.
[2023-03-17 00:46:08,083] [INFO] Target genome list was writen to OceanDNA-b45620/target_genomes.txt
[2023-03-17 00:46:08,130] [INFO] Task started: fastANI
[2023-03-17 00:46:08,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg967511be-ba25-4a53-8afa-987d2e98a842/OceanDNA-b45620.fa --refList OceanDNA-b45620/target_genomes.txt --output OceanDNA-b45620/fastani_result.tsv --threads 1
[2023-03-17 00:46:13,566] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:13,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:13,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:13,567] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:13,567] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:13,567] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:13,567] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45620/tc_result.tsv
[2023-03-17 00:46:13,567] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:13,567] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:13,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference/checkm_data
[2023-03-17 00:46:13,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:13,574] [INFO] Task started: CheckM
[2023-03-17 00:46:13,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45620/checkm_input OceanDNA-b45620/checkm_result
[2023-03-17 00:47:03,885] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:03,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:03,888] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:03,888] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:03,888] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45620/markers.fasta)
[2023-03-17 00:47:03,888] [INFO] Task started: Blastn
[2023-03-17 00:47:03,889] [INFO] Running command: blastn -query OceanDNA-b45620/markers.fasta -db /var/lib/cwl/stg25f63acf-61f2-4453-893d-5877bf1600ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:04,826] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:04,827] [INFO] Selected 26 target genomes.
[2023-03-17 00:47:04,827] [INFO] Target genome list was writen to OceanDNA-b45620/target_genomes_gtdb.txt
[2023-03-17 00:47:05,422] [INFO] Task started: fastANI
[2023-03-17 00:47:05,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg967511be-ba25-4a53-8afa-987d2e98a842/OceanDNA-b45620.fa --refList OceanDNA-b45620/target_genomes_gtdb.txt --output OceanDNA-b45620/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:17,870] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:17,874] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:17,875] [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_902580225.1	s__MB11C04 sp902580225	80.3449	156	801	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478775.1	s__MB11C04 sp002477515	78.566	217	801	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.93	98.38	0.86	0.80	5	-
GCA_002167265.1	s__MB11C04 sp002167265	78.3692	56	801	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675995.1	s__MB11C04 sp018675995	78.3389	115	801	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645475.1	s__MB11C04 sp018645475	78.2486	150	801	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364975.1	s__MB11C04 sp002364975	77.7072	56	801	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.20	99.18	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:17,875] [INFO] GTDB search result was written to OceanDNA-b45620/result_gtdb.tsv
[2023-03-17 00:47:17,875] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:17,875] [INFO] DFAST_QC result json was written to OceanDNA-b45620/dqc_result.json
[2023-03-17 00:47:17,876] [INFO] DFAST_QC completed!
[2023-03-17 00:47:17,876] [INFO] Total running time: 0h1m31s