[2023-03-17 03:50:13,764] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference
[2023-03-17 03:50:15,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,140] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,140] [INFO] Running command: cat /var/lib/cwl/stgb3fa881b-8a79-4a2b-b114-37182bbc7338/OceanDNA-b17186.fa | prodigal -d OceanDNA-b17186/cds.fna -a OceanDNA-b17186/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:32,055] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:32,055] [INFO] Task started: HMMsearch
[2023-03-17 03:50:32,055] [INFO] Running command: hmmsearch --tblout OceanDNA-b17186/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference/reference_markers.hmm OceanDNA-b17186/protein.faa > /dev/null
[2023-03-17 03:50:32,268] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:32,269] [INFO] Found 6/6 markers.
[2023-03-17 03:50:32,291] [INFO] Query marker FASTA was written to OceanDNA-b17186/markers.fasta
[2023-03-17 03:50:32,291] [INFO] Task started: Blastn
[2023-03-17 03:50:32,291] [INFO] Running command: blastn -query OceanDNA-b17186/markers.fasta -db /var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference/reference_markers.fasta -out OceanDNA-b17186/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:32,844] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:32,845] [INFO] Selected 6 target genomes.
[2023-03-17 03:50:32,845] [INFO] Target genome list was writen to OceanDNA-b17186/target_genomes.txt
[2023-03-17 03:50:32,848] [INFO] Task started: fastANI
[2023-03-17 03:50:32,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3fa881b-8a79-4a2b-b114-37182bbc7338/OceanDNA-b17186.fa --refList OceanDNA-b17186/target_genomes.txt --output OceanDNA-b17186/fastani_result.tsv --threads 1
[2023-03-17 03:50:37,637] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:37,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:37,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:37,643] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 03:50:37,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 03:50:37,643] [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
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	97.1169	736	1129	95	conclusive
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	94.9526	840	1129	95	below_threshold
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	94.8423	817	1129	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	94.8045	841	1129	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	94.555	828	1129	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	94.5447	839	1129	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:37,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17186/tc_result.tsv
[2023-03-17 03:50:37,643] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:37,643] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:37,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference/checkm_data
[2023-03-17 03:50:37,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:37,649] [INFO] Task started: CheckM
[2023-03-17 03:50:37,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17186/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17186/checkm_input OceanDNA-b17186/checkm_result
[2023-03-17 03:51:21,088] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:21,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:21,090] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:21,091] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:21,091] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17186/markers.fasta)
[2023-03-17 03:51:21,091] [INFO] Task started: Blastn
[2023-03-17 03:51:21,091] [INFO] Running command: blastn -query OceanDNA-b17186/markers.fasta -db /var/lib/cwl/stg6387ee29-2fb2-46ed-a537-f1680c1ea30e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17186/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:21,987] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:21,988] [INFO] Selected 5 target genomes.
[2023-03-17 03:51:21,988] [INFO] Target genome list was writen to OceanDNA-b17186/target_genomes_gtdb.txt
[2023-03-17 03:51:21,991] [INFO] Task started: fastANI
[2023-03-17 03:51:21,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3fa881b-8a79-4a2b-b114-37182bbc7338/OceanDNA-b17186.fa --refList OceanDNA-b17186/target_genomes_gtdb.txt --output OceanDNA-b17186/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:25,934] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:25,938] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:51:25,938] [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
GCF_001006285.1	s__Paraclostridium benzoelyticum	97.1247	735	1129	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.4733	N/A	N/A	N/A	N/A	1	conclusive
GCF_006802875.1	s__Paraclostridium bifermentans	94.7803	842	1129	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_000452245.2	s__Paraclostridium bifermentans_A	94.5447	839	1129	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
GCF_015668515.1	s__Paraclostridium tenue	83.3218	555	1129	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_000953675.1	s__Paraclostridium sordellii	82.7948	563	1129	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:25,938] [INFO] GTDB search result was written to OceanDNA-b17186/result_gtdb.tsv
[2023-03-17 03:51:25,938] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:25,939] [INFO] DFAST_QC result json was written to OceanDNA-b17186/dqc_result.json
[2023-03-17 03:51:25,939] [INFO] DFAST_QC completed!
[2023-03-17 03:51:25,939] [INFO] Total running time: 0h1m12s