[2023-03-15 09:48:16,561] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,228] [INFO] Running command: cat /var/lib/cwl/stgd5e6d378-9272-4772-a93d-1a0ad94597c9/OceanDNA-b13561.fa | prodigal -d OceanDNA-b13561/cds.fna -a OceanDNA-b13561/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:32,878] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:32,879] [INFO] Task started: HMMsearch
[2023-03-15 09:48:32,879] [INFO] Running command: hmmsearch --tblout OceanDNA-b13561/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference/reference_markers.hmm OceanDNA-b13561/protein.faa > /dev/null
[2023-03-15 09:48:33,080] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:33,081] [INFO] Found 6/6 markers.
[2023-03-15 09:48:33,100] [INFO] Query marker FASTA was written to OceanDNA-b13561/markers.fasta
[2023-03-15 09:48:33,100] [INFO] Task started: Blastn
[2023-03-15 09:48:33,100] [INFO] Running command: blastn -query OceanDNA-b13561/markers.fasta -db /var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference/reference_markers.fasta -out OceanDNA-b13561/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:33,645] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:33,645] [INFO] Selected 21 target genomes.
[2023-03-15 09:48:33,646] [INFO] Target genome list was writen to OceanDNA-b13561/target_genomes.txt
[2023-03-15 09:48:33,658] [INFO] Task started: fastANI
[2023-03-15 09:48:33,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e6d378-9272-4772-a93d-1a0ad94597c9/OceanDNA-b13561.fa --refList OceanDNA-b13561/target_genomes.txt --output OceanDNA-b13561/fastani_result.tsv --threads 1
[2023-03-15 09:48:45,917] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:45,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:45,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:45,918] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:45,918] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:45,918] [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 09:48:45,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13561/tc_result.tsv
[2023-03-15 09:48:45,918] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:45,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:45,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference/checkm_data
[2023-03-15 09:48:45,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:45,937] [INFO] Task started: CheckM
[2023-03-15 09:48:45,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13561/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13561/checkm_input OceanDNA-b13561/checkm_result
[2023-03-15 09:49:25,553] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:25,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:25,556] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:25,556] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:25,557] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13561/markers.fasta)
[2023-03-15 09:49:25,557] [INFO] Task started: Blastn
[2023-03-15 09:49:25,557] [INFO] Running command: blastn -query OceanDNA-b13561/markers.fasta -db /var/lib/cwl/stg638575b5-017b-4f02-b2db-d5d793a478c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13561/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:26,420] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:26,421] [INFO] Selected 18 target genomes.
[2023-03-15 09:49:26,421] [INFO] Target genome list was writen to OceanDNA-b13561/target_genomes_gtdb.txt
[2023-03-15 09:49:26,828] [INFO] Task started: fastANI
[2023-03-15 09:49:26,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e6d378-9272-4772-a93d-1a0ad94597c9/OceanDNA-b13561.fa --refList OceanDNA-b13561/target_genomes_gtdb.txt --output OceanDNA-b13561/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:37,643] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:37,647] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:49:37,647] [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_018648655.1	s__Desulfolinea sp018648655	99.7355	693	866	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.77	99.77	0.84	0.82	3	conclusive
GCA_018645405.1	s__Desulfolinea sp018645405	80.1831	383	866	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.86	99.73	0.91	0.78	10	-
GCA_016744335.1	s__Desulfolinea sp016744335	79.7237	466	866	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382535.1	s__Desulfolinea nitratireducens	76.1397	116	866	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.72	99.72	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:37,647] [INFO] GTDB search result was written to OceanDNA-b13561/result_gtdb.tsv
[2023-03-15 09:49:37,647] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:37,648] [INFO] DFAST_QC result json was written to OceanDNA-b13561/dqc_result.json
[2023-03-15 09:49:37,648] [INFO] DFAST_QC completed!
[2023-03-15 09:49:37,648] [INFO] Total running time: 0h1m21s