[2023-03-19 05:19:33,766] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference
[2023-03-19 05:19:35,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,401] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,402] [INFO] Running command: cat /var/lib/cwl/stg629b64af-8ff0-450c-84f5-ce44d0ae60a2/OceanDNA-b20979.fa | prodigal -d OceanDNA-b20979/cds.fna -a OceanDNA-b20979/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:20:00,571] [INFO] Task succeeded: Prodigal
[2023-03-19 05:20:00,572] [INFO] Task started: HMMsearch
[2023-03-19 05:20:00,572] [INFO] Running command: hmmsearch --tblout OceanDNA-b20979/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference/reference_markers.hmm OceanDNA-b20979/protein.faa > /dev/null
[2023-03-19 05:20:00,863] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:20:00,864] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg629b64af-8ff0-450c-84f5-ce44d0ae60a2/OceanDNA-b20979.fa]
[2023-03-19 05:20:00,890] [INFO] Query marker FASTA was written to OceanDNA-b20979/markers.fasta
[2023-03-19 05:20:00,890] [INFO] Task started: Blastn
[2023-03-19 05:20:00,890] [INFO] Running command: blastn -query OceanDNA-b20979/markers.fasta -db /var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference/reference_markers.fasta -out OceanDNA-b20979/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:01,453] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:01,454] [INFO] Selected 31 target genomes.
[2023-03-19 05:20:01,454] [INFO] Target genome list was writen to OceanDNA-b20979/target_genomes.txt
[2023-03-19 05:20:01,486] [INFO] Task started: fastANI
[2023-03-19 05:20:01,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg629b64af-8ff0-450c-84f5-ce44d0ae60a2/OceanDNA-b20979.fa --refList OceanDNA-b20979/target_genomes.txt --output OceanDNA-b20979/fastani_result.tsv --threads 1
[2023-03-19 05:20:25,232] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:25,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:25,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:25,233] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:25,233] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:20:25,233] [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 05:20:25,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20979/tc_result.tsv
[2023-03-19 05:20:25,233] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:25,234] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:25,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference/checkm_data
[2023-03-19 05:20:25,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:25,245] [INFO] Task started: CheckM
[2023-03-19 05:20:25,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20979/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20979/checkm_input OceanDNA-b20979/checkm_result
[2023-03-19 05:21:26,278] [INFO] Task succeeded: CheckM
[2023-03-19 05:21:26,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:21:26,282] [INFO] ===== Completeness check finished =====
[2023-03-19 05:21:26,282] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:21:26,282] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20979/markers.fasta)
[2023-03-19 05:21:26,282] [INFO] Task started: Blastn
[2023-03-19 05:21:26,282] [INFO] Running command: blastn -query OceanDNA-b20979/markers.fasta -db /var/lib/cwl/stg373489b6-e77f-4b09-9273-a22a8d13f217/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20979/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:21:27,060] [INFO] Task succeeded: Blastn
[2023-03-19 05:21:27,061] [INFO] Selected 29 target genomes.
[2023-03-19 05:21:27,061] [INFO] Target genome list was writen to OceanDNA-b20979/target_genomes_gtdb.txt
[2023-03-19 05:21:27,242] [INFO] Task started: fastANI
[2023-03-19 05:21:27,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg629b64af-8ff0-450c-84f5-ce44d0ae60a2/OceanDNA-b20979.fa --refList OceanDNA-b20979/target_genomes_gtdb.txt --output OceanDNA-b20979/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:48,787] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:48,791] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:21:48,791] [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_002433485.1	s__UBA6601 sp002433485	99.9011	1291	1362	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__UBA6601	95.0	99.91	99.91	0.95	0.95	2	conclusive
GCA_002724675.1	s__GCA-2724675 sp002724675	76.1752	130	1362	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__GCA-2724675	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401435.1	s__M30B51 sp018401435	75.234	56	1362	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.2194	54	1362	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:48,791] [INFO] GTDB search result was written to OceanDNA-b20979/result_gtdb.tsv
[2023-03-19 05:21:48,791] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:48,792] [INFO] DFAST_QC result json was written to OceanDNA-b20979/dqc_result.json
[2023-03-19 05:21:48,792] [INFO] DFAST_QC completed!
[2023-03-19 05:21:48,792] [INFO] Total running time: 0h2m15s