[2023-03-15 18:39:12,219] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference
[2023-03-15 18:39:13,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg9edc60f3-9eef-4861-88ce-01eb7351304d/OceanDNA-b15665.fa | prodigal -d OceanDNA-b15665/cds.fna -a OceanDNA-b15665/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:25,936] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:25,937] [INFO] Task started: HMMsearch
[2023-03-15 18:39:25,937] [INFO] Running command: hmmsearch --tblout OceanDNA-b15665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference/reference_markers.hmm OceanDNA-b15665/protein.faa > /dev/null
[2023-03-15 18:39:26,104] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:26,104] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9edc60f3-9eef-4861-88ce-01eb7351304d/OceanDNA-b15665.fa]
[2023-03-15 18:39:26,118] [INFO] Query marker FASTA was written to OceanDNA-b15665/markers.fasta
[2023-03-15 18:39:26,119] [INFO] Task started: Blastn
[2023-03-15 18:39:26,119] [INFO] Running command: blastn -query OceanDNA-b15665/markers.fasta -db /var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference/reference_markers.fasta -out OceanDNA-b15665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:26,601] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:26,601] [INFO] Selected 10 target genomes.
[2023-03-15 18:39:26,602] [INFO] Target genome list was writen to OceanDNA-b15665/target_genomes.txt
[2023-03-15 18:39:26,607] [INFO] Task started: fastANI
[2023-03-15 18:39:26,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg9edc60f3-9eef-4861-88ce-01eb7351304d/OceanDNA-b15665.fa --refList OceanDNA-b15665/target_genomes.txt --output OceanDNA-b15665/fastani_result.tsv --threads 1
[2023-03-15 18:39:31,967] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:31,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:31,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:31,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:31,968] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:31,968] [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
--------------------------------------------------------------------------------
[2023-03-15 18:39:31,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15665/tc_result.tsv
[2023-03-15 18:39:31,968] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:31,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:31,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference/checkm_data
[2023-03-15 18:39:31,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:31,974] [INFO] Task started: CheckM
[2023-03-15 18:39:31,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15665/checkm_input OceanDNA-b15665/checkm_result
[2023-03-15 18:40:05,700] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:05,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.10%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:05,702] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:05,703] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:05,703] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15665/markers.fasta)
[2023-03-15 18:40:05,703] [INFO] Task started: Blastn
[2023-03-15 18:40:05,703] [INFO] Running command: blastn -query OceanDNA-b15665/markers.fasta -db /var/lib/cwl/stg979dafb2-fc7d-45cb-bf53-e169d85bfd80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:06,305] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:06,306] [INFO] Selected 18 target genomes.
[2023-03-15 18:40:06,306] [INFO] Target genome list was writen to OceanDNA-b15665/target_genomes_gtdb.txt
[2023-03-15 18:40:06,883] [INFO] Task started: fastANI
[2023-03-15 18:40:06,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg9edc60f3-9eef-4861-88ce-01eb7351304d/OceanDNA-b15665.fa --refList OceanDNA-b15665/target_genomes_gtdb.txt --output OceanDNA-b15665/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:14,024] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:14,029] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:40:14,029] [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_002730485.1	s__UBA9611 sp002730485	78.8075	321	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959605.1	s__UBA9611 sp012959605	77.4199	226	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.56	99.56	0.90	0.90	2	-
GCA_002328185.1	s__UBA9611 sp002328185	76.6182	133	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_002721995.1	s__UBA9611 sp002721995	76.3876	75	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002698265.1	s__UBA9611 sp002698265	76.1937	86	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
GCA_002746355.1	s__UBA9611 sp002746355	76.0944	130	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_013204585.1	s__UBA9611 sp013204585	76.0168	93	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002816575.1	s__UBA9611 sp002816575	75.9277	69	693	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:14,030] [INFO] GTDB search result was written to OceanDNA-b15665/result_gtdb.tsv
[2023-03-15 18:40:14,030] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:14,031] [INFO] DFAST_QC result json was written to OceanDNA-b15665/dqc_result.json
[2023-03-15 18:40:14,031] [INFO] DFAST_QC completed!
[2023-03-15 18:40:14,031] [INFO] Total running time: 0h1m2s