[2023-03-18 04:04:53,869] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,869] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,869] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference
[2023-03-18 04:04:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stg32eb90d2-ea92-4af2-b2a1-24c15ab3a6e1/OceanDNA-b17240.fa | prodigal -d OceanDNA-b17240/cds.fna -a OceanDNA-b17240/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:03,354] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:03,354] [INFO] Task started: HMMsearch
[2023-03-18 04:05:03,354] [INFO] Running command: hmmsearch --tblout OceanDNA-b17240/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference/reference_markers.hmm OceanDNA-b17240/protein.faa > /dev/null
[2023-03-18 04:05:03,529] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:03,529] [INFO] Found 6/6 markers.
[2023-03-18 04:05:03,543] [INFO] Query marker FASTA was written to OceanDNA-b17240/markers.fasta
[2023-03-18 04:05:03,543] [INFO] Task started: Blastn
[2023-03-18 04:05:03,543] [INFO] Running command: blastn -query OceanDNA-b17240/markers.fasta -db /var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference/reference_markers.fasta -out OceanDNA-b17240/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:04,092] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:04,093] [INFO] Selected 11 target genomes.
[2023-03-18 04:05:04,093] [INFO] Target genome list was writen to OceanDNA-b17240/target_genomes.txt
[2023-03-18 04:05:04,100] [INFO] Task started: fastANI
[2023-03-18 04:05:04,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg32eb90d2-ea92-4af2-b2a1-24c15ab3a6e1/OceanDNA-b17240.fa --refList OceanDNA-b17240/target_genomes.txt --output OceanDNA-b17240/fastani_result.tsv --threads 1
[2023-03-18 04:05:09,296] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:09,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:09,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:09,297] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:09,297] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:05:09,297] [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
--------------------------------------------------------------------------------
[2023-03-18 04:05:09,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17240/tc_result.tsv
[2023-03-18 04:05:09,298] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:09,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:09,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference/checkm_data
[2023-03-18 04:05:09,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:09,346] [INFO] Task started: CheckM
[2023-03-18 04:05:09,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17240/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17240/checkm_input OceanDNA-b17240/checkm_result
[2023-03-18 04:05:35,248] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:35,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:35,256] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:35,256] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:35,256] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17240/markers.fasta)
[2023-03-18 04:05:35,256] [INFO] Task started: Blastn
[2023-03-18 04:05:35,256] [INFO] Running command: blastn -query OceanDNA-b17240/markers.fasta -db /var/lib/cwl/stgbbb8c467-cb56-4887-b795-c030f86866ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17240/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:36,142] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:36,143] [INFO] Selected 19 target genomes.
[2023-03-18 04:05:36,143] [INFO] Target genome list was writen to OceanDNA-b17240/target_genomes_gtdb.txt
[2023-03-18 04:05:36,607] [INFO] Task started: fastANI
[2023-03-18 04:05:36,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg32eb90d2-ea92-4af2-b2a1-24c15ab3a6e1/OceanDNA-b17240.fa --refList OceanDNA-b17240/target_genomes_gtdb.txt --output OceanDNA-b17240/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:05:47,315] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:47,318] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:05:47,318] [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_002718595.1	s__GCA-2718595 sp002718595	92.8319	458	483	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__GCA-2718595	95.0	97.60	97.14	0.94	0.91	9	-
GCA_012959595.1	s__GCA-2718595 sp012959595	78.2625	125	483	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__GCA-2718595	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:05:47,319] [INFO] GTDB search result was written to OceanDNA-b17240/result_gtdb.tsv
[2023-03-18 04:05:47,319] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:05:47,321] [INFO] DFAST_QC result json was written to OceanDNA-b17240/dqc_result.json
[2023-03-18 04:05:47,321] [INFO] DFAST_QC completed!
[2023-03-18 04:05:47,321] [INFO] Total running time: 0h0m53s