[2023-03-14 13:05:30,729] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:05:30,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:05:30,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference
[2023-03-14 13:05:31,958] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:05:31,959] [INFO] Task started: Prodigal
[2023-03-14 13:05:31,959] [INFO] Running command: cat /var/lib/cwl/stg39b684ef-2e7d-44c6-9a3f-120d08021633/OceanDNA-b46923.fa | prodigal -d OceanDNA-b46923/cds.fna -a OceanDNA-b46923/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:06:01,372] [INFO] Task succeeded: Prodigal
[2023-03-14 13:06:01,372] [INFO] Task started: HMMsearch
[2023-03-14 13:06:01,372] [INFO] Running command: hmmsearch --tblout OceanDNA-b46923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference/reference_markers.hmm OceanDNA-b46923/protein.faa > /dev/null
[2023-03-14 13:06:01,562] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:06:01,563] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg39b684ef-2e7d-44c6-9a3f-120d08021633/OceanDNA-b46923.fa]
[2023-03-14 13:06:01,592] [INFO] Query marker FASTA was written to OceanDNA-b46923/markers.fasta
[2023-03-14 13:06:01,593] [INFO] Task started: Blastn
[2023-03-14 13:06:01,593] [INFO] Running command: blastn -query OceanDNA-b46923/markers.fasta -db /var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference/reference_markers.fasta -out OceanDNA-b46923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:06:02,024] [INFO] Task succeeded: Blastn
[2023-03-14 13:06:02,025] [INFO] Selected 20 target genomes.
[2023-03-14 13:06:02,025] [INFO] Target genome list was writen to OceanDNA-b46923/target_genomes.txt
[2023-03-14 13:06:02,049] [INFO] Task started: fastANI
[2023-03-14 13:06:02,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b684ef-2e7d-44c6-9a3f-120d08021633/OceanDNA-b46923.fa --refList OceanDNA-b46923/target_genomes.txt --output OceanDNA-b46923/fastani_result.tsv --threads 1
[2023-03-14 13:06:16,336] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:16,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:06:16,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:06:16,336] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:06:16,336] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:06:16,336] [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
--------------------------------------------------------------------------------
[2023-03-14 13:06:16,337] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46923/tc_result.tsv
[2023-03-14 13:06:16,337] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:06:16,337] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:06:16,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference/checkm_data
[2023-03-14 13:06:16,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:06:16,346] [INFO] Task started: CheckM
[2023-03-14 13:06:16,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46923/checkm_input OceanDNA-b46923/checkm_result
[2023-03-14 13:07:55,253] [INFO] Task succeeded: CheckM
[2023-03-14 13:07:55,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:07:55,257] [INFO] ===== Completeness check finished =====
[2023-03-14 13:07:55,257] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:07:55,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46923/markers.fasta)
[2023-03-14 13:07:55,282] [INFO] Task started: Blastn
[2023-03-14 13:07:55,282] [INFO] Running command: blastn -query OceanDNA-b46923/markers.fasta -db /var/lib/cwl/stg6bf683bd-8607-4f6c-b0a2-b34e6168af50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:07:56,066] [INFO] Task succeeded: Blastn
[2023-03-14 13:07:56,068] [INFO] Selected 15 target genomes.
[2023-03-14 13:07:56,068] [INFO] Target genome list was writen to OceanDNA-b46923/target_genomes_gtdb.txt
[2023-03-14 13:07:56,080] [INFO] Task started: fastANI
[2023-03-14 13:07:56,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b684ef-2e7d-44c6-9a3f-120d08021633/OceanDNA-b46923.fa --refList OceanDNA-b46923/target_genomes_gtdb.txt --output OceanDNA-b46923/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:08:06,271] [INFO] Task succeeded: fastANI
[2023-03-14 13:08:06,277] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:08:06,277] [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_002862135.1	s__Arctic95D-9 sp002862135	76.2121	58	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213905.1	s__Arctic95D-9 sp013213905	76.0458	95	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422425.1	s__Arctic95D-9 sp002422425	75.9525	75	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991025.1	s__Arctic95D-9 sp017991025	75.7713	61	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058245.1	s__Arctic95D-9 sp018058245	75.767	74	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	99.34	99.34	0.85	0.85	2	-
GCA_002344215.1	s__Arctic95D-9 sp002344215	75.7418	80	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396885.1	s__Arctic95D-9 sp002396885	75.5806	70	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	75.4706	64	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344525.1	s__Arctic95D-9 sp002344525	75.3534	56	1175	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:08:06,278] [INFO] GTDB search result was written to OceanDNA-b46923/result_gtdb.tsv
[2023-03-14 13:08:06,279] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:08:06,279] [INFO] DFAST_QC result json was written to OceanDNA-b46923/dqc_result.json
[2023-03-14 13:08:06,280] [INFO] DFAST_QC completed!
[2023-03-14 13:08:06,280] [INFO] Total running time: 0h2m36s