[2023-03-15 19:39:19,144] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:39:19,145] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:39:19,145] [INFO] DQC Reference Directory: /var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference
[2023-03-15 19:39:22,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:39:22,367] [INFO] Task started: Prodigal
[2023-03-15 19:39:22,367] [INFO] Running command: cat /var/lib/cwl/stgacb16ba8-879e-412a-9006-00fca3022298/OceanDNA-b42803.fa | prodigal -d OceanDNA-b42803/cds.fna -a OceanDNA-b42803/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:39:26,732] [INFO] Task succeeded: Prodigal
[2023-03-15 19:39:26,732] [INFO] Task started: HMMsearch
[2023-03-15 19:39:26,732] [INFO] Running command: hmmsearch --tblout OceanDNA-b42803/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference/reference_markers.hmm OceanDNA-b42803/protein.faa > /dev/null
[2023-03-15 19:39:26,952] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:39:26,953] [INFO] Found 6/6 markers.
[2023-03-15 19:39:26,961] [INFO] Query marker FASTA was written to OceanDNA-b42803/markers.fasta
[2023-03-15 19:39:26,961] [INFO] Task started: Blastn
[2023-03-15 19:39:26,961] [INFO] Running command: blastn -query OceanDNA-b42803/markers.fasta -db /var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference/reference_markers.fasta -out OceanDNA-b42803/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:39:30,098] [INFO] Task succeeded: Blastn
[2023-03-15 19:39:30,099] [INFO] Selected 12 target genomes.
[2023-03-15 19:39:30,099] [INFO] Target genome list was writen to OceanDNA-b42803/target_genomes.txt
[2023-03-15 19:39:30,108] [INFO] Task started: fastANI
[2023-03-15 19:39:30,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb16ba8-879e-412a-9006-00fca3022298/OceanDNA-b42803.fa --refList OceanDNA-b42803/target_genomes.txt --output OceanDNA-b42803/fastani_result.tsv --threads 1
[2023-03-15 19:39:33,487] [INFO] Task succeeded: fastANI
[2023-03-15 19:39:33,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:39:33,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:39:33,487] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:39:33,488] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 19:39:33,488] [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 19:39:33,488] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42803/tc_result.tsv
[2023-03-15 19:39:33,488] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:39:33,488] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:39:33,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference/checkm_data
[2023-03-15 19:39:33,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:39:33,540] [INFO] Task started: CheckM
[2023-03-15 19:39:33,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42803/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42803/checkm_input OceanDNA-b42803/checkm_result
[2023-03-15 19:39:58,940] [INFO] Task succeeded: CheckM
[2023-03-15 19:39:58,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 19:39:58,941] [INFO] ===== Completeness check finished =====
[2023-03-15 19:39:58,941] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:39:58,942] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42803/markers.fasta)
[2023-03-15 19:39:58,943] [INFO] Task started: Blastn
[2023-03-15 19:39:58,943] [INFO] Running command: blastn -query OceanDNA-b42803/markers.fasta -db /var/lib/cwl/stgc40495a5-2de4-4fcd-ab19-29bfd44527c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42803/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:40:00,516] [INFO] Task succeeded: Blastn
[2023-03-15 19:40:00,517] [INFO] Selected 17 target genomes.
[2023-03-15 19:40:00,517] [INFO] Target genome list was writen to OceanDNA-b42803/target_genomes_gtdb.txt
[2023-03-15 19:40:01,340] [INFO] Task started: fastANI
[2023-03-15 19:40:01,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb16ba8-879e-412a-9006-00fca3022298/OceanDNA-b42803.fa --refList OceanDNA-b42803/target_genomes_gtdb.txt --output OceanDNA-b42803/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:40:04,429] [INFO] Task succeeded: fastANI
[2023-03-15 19:40:04,435] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 19:40:04,435] [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_002684055.1	s__TMED112 sp002684055	96.7227	138	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004321845.1	s__TMED112 sp004321845	81.801	100	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213455.1	s__TMED112 sp003213455	81.4334	96	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902619265.1	s__TMED112 sp902619265	78.1951	102	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.88	96.64	0.91	0.88	6	-
GCA_002683115.1	s__TMED112 sp002683115	78.1395	68	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278815.1	s__TMED112 sp003278815	78.1166	86	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902585315.1	s__TMED112 sp902585315	77.903	79	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.21	96.04	0.78	0.78	6	-
GCA_002692425.1	s__TMED112 sp002692425	77.7278	50	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535365.1	s__TMED112 sp902535365	77.1902	55	189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.49	95.14	0.87	0.82	7	-
--------------------------------------------------------------------------------
[2023-03-15 19:40:04,436] [INFO] GTDB search result was written to OceanDNA-b42803/result_gtdb.tsv
[2023-03-15 19:40:04,436] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:40:04,437] [INFO] DFAST_QC result json was written to OceanDNA-b42803/dqc_result.json
[2023-03-15 19:40:04,437] [INFO] DFAST_QC completed!
[2023-03-15 19:40:04,437] [INFO] Total running time: 0h0m45s