[2023-03-18 07:29:29,819] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,820] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,820] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference
[2023-03-18 07:29:30,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,929] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,929] [INFO] Running command: cat /var/lib/cwl/stg7c2a8a81-2513-4016-89ff-f24cebcfcda4/OceanDNA-b18437.fa | prodigal -d OceanDNA-b18437/cds.fna -a OceanDNA-b18437/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:42,910] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:42,911] [INFO] Task started: HMMsearch
[2023-03-18 07:29:42,911] [INFO] Running command: hmmsearch --tblout OceanDNA-b18437/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference/reference_markers.hmm OceanDNA-b18437/protein.faa > /dev/null
[2023-03-18 07:29:43,079] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:43,079] [INFO] Found 6/6 markers.
[2023-03-18 07:29:43,094] [INFO] Query marker FASTA was written to OceanDNA-b18437/markers.fasta
[2023-03-18 07:29:43,094] [INFO] Task started: Blastn
[2023-03-18 07:29:43,094] [INFO] Running command: blastn -query OceanDNA-b18437/markers.fasta -db /var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference/reference_markers.fasta -out OceanDNA-b18437/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:43,600] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:43,601] [INFO] Selected 18 target genomes.
[2023-03-18 07:29:43,601] [INFO] Target genome list was writen to OceanDNA-b18437/target_genomes.txt
[2023-03-18 07:29:43,610] [INFO] Task started: fastANI
[2023-03-18 07:29:43,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2a8a81-2513-4016-89ff-f24cebcfcda4/OceanDNA-b18437.fa --refList OceanDNA-b18437/target_genomes.txt --output OceanDNA-b18437/fastani_result.tsv --threads 1
[2023-03-18 07:29:52,049] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:52,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:52,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:52,050] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:52,050] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:52,050] [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 07:29:52,050] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18437/tc_result.tsv
[2023-03-18 07:29:52,050] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:52,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:52,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference/checkm_data
[2023-03-18 07:29:52,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:52,058] [INFO] Task started: CheckM
[2023-03-18 07:29:52,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18437/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18437/checkm_input OceanDNA-b18437/checkm_result
[2023-03-18 07:30:26,739] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:26,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:26,741] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:26,741] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:26,742] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18437/markers.fasta)
[2023-03-18 07:30:26,742] [INFO] Task started: Blastn
[2023-03-18 07:30:26,742] [INFO] Running command: blastn -query OceanDNA-b18437/markers.fasta -db /var/lib/cwl/stgfdbeb73c-afc8-4cff-9810-cd38d21313c8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18437/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:27,614] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:27,615] [INFO] Selected 15 target genomes.
[2023-03-18 07:30:27,615] [INFO] Target genome list was writen to OceanDNA-b18437/target_genomes_gtdb.txt
[2023-03-18 07:30:27,854] [INFO] Task started: fastANI
[2023-03-18 07:30:27,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2a8a81-2513-4016-89ff-f24cebcfcda4/OceanDNA-b18437.fa --refList OceanDNA-b18437/target_genomes_gtdb.txt --output OceanDNA-b18437/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:34,262] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:34,265] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:30:34,265] [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_002329125.1	s__UBA2125 sp002329125	99.711	489	687	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	97.65	95.42	0.79	0.68	5	conclusive
GCA_004124465.1	s__UBA2125 sp004124465	94.6621	330	687	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964825.1	s__UBA2125 sp002311275	85.2316	491	687	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	99.57	99.39	0.92	0.84	10	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:34,265] [INFO] GTDB search result was written to OceanDNA-b18437/result_gtdb.tsv
[2023-03-18 07:30:34,265] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:34,266] [INFO] DFAST_QC result json was written to OceanDNA-b18437/dqc_result.json
[2023-03-18 07:30:34,266] [INFO] DFAST_QC completed!
[2023-03-18 07:30:34,266] [INFO] Total running time: 0h1m4s