[2023-03-15 15:51:29,967] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference
[2023-03-15 15:51:31,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,680] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stg405b84cf-65ba-4e11-bef8-bb96d5223886/OceanDNA-b46964.fa | prodigal -d OceanDNA-b46964/cds.fna -a OceanDNA-b46964/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:47,315] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:47,315] [INFO] Task started: HMMsearch
[2023-03-15 15:51:47,315] [INFO] Running command: hmmsearch --tblout OceanDNA-b46964/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference/reference_markers.hmm OceanDNA-b46964/protein.faa > /dev/null
[2023-03-15 15:51:47,506] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:47,507] [INFO] Found 6/6 markers.
[2023-03-15 15:51:47,530] [INFO] Query marker FASTA was written to OceanDNA-b46964/markers.fasta
[2023-03-15 15:51:47,530] [INFO] Task started: Blastn
[2023-03-15 15:51:47,530] [INFO] Running command: blastn -query OceanDNA-b46964/markers.fasta -db /var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference/reference_markers.fasta -out OceanDNA-b46964/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:48,079] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:48,080] [INFO] Selected 11 target genomes.
[2023-03-15 15:51:48,080] [INFO] Target genome list was writen to OceanDNA-b46964/target_genomes.txt
[2023-03-15 15:51:48,087] [INFO] Task started: fastANI
[2023-03-15 15:51:48,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg405b84cf-65ba-4e11-bef8-bb96d5223886/OceanDNA-b46964.fa --refList OceanDNA-b46964/target_genomes.txt --output OceanDNA-b46964/fastani_result.tsv --threads 1
[2023-03-15 15:51:51,521] [INFO] Task succeeded: fastANI
[2023-03-15 15:51:51,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:51:51,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:51:51,521] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:51:51,522] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:51:51,522] [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 15:51:51,522] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46964/tc_result.tsv
[2023-03-15 15:51:51,522] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:51:51,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:51:51,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference/checkm_data
[2023-03-15 15:51:51,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:51:51,533] [INFO] Task started: CheckM
[2023-03-15 15:51:51,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46964/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46964/checkm_input OceanDNA-b46964/checkm_result
[2023-03-15 15:52:35,934] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:35,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:35,937] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:35,937] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:35,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46964/markers.fasta)
[2023-03-15 15:52:35,938] [INFO] Task started: Blastn
[2023-03-15 15:52:35,939] [INFO] Running command: blastn -query OceanDNA-b46964/markers.fasta -db /var/lib/cwl/stg03045112-aca5-4b87-a0a2-fa4b7fc8a89d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46964/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:36,839] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:36,840] [INFO] Selected 11 target genomes.
[2023-03-15 15:52:36,840] [INFO] Target genome list was writen to OceanDNA-b46964/target_genomes_gtdb.txt
[2023-03-15 15:52:36,854] [INFO] Task started: fastANI
[2023-03-15 15:52:36,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg405b84cf-65ba-4e11-bef8-bb96d5223886/OceanDNA-b46964.fa --refList OceanDNA-b46964/target_genomes_gtdb.txt --output OceanDNA-b46964/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:52:42,072] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:42,076] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:52:42,077] [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_902591645.1	s__EC70 sp902591645	94.7103	304	547	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	95.33	95.33	0.70	0.70	2	-
GCA_012960505.1	s__EC70 sp012960505	88.6463	520	547	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	99.96	99.96	0.97	0.97	2	-
GCA_014239335.1	s__EC70 sp014239335	87.7483	349	547	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.68	98.68	0.76	0.76	2	-
GCA_004211885.1	s__EC70 sp004211885	86.5629	441	547	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213965.1	s__EC70 sp013213965	84.5055	393	547	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708885.1	s__EC70 sp002708885	82.2474	399	547	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.95	98.84	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-15 15:52:42,077] [INFO] GTDB search result was written to OceanDNA-b46964/result_gtdb.tsv
[2023-03-15 15:52:42,077] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:52:42,078] [INFO] DFAST_QC result json was written to OceanDNA-b46964/dqc_result.json
[2023-03-15 15:52:42,078] [INFO] DFAST_QC completed!
[2023-03-15 15:52:42,078] [INFO] Total running time: 0h1m12s