[2023-03-17 05:34:58,189] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,190] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference
[2023-03-17 05:34:59,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,323] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,323] [INFO] Running command: cat /var/lib/cwl/stgb4f6530f-bbb9-41c5-87b1-7d98b203cd73/OceanDNA-b35988.fa | prodigal -d OceanDNA-b35988/cds.fna -a OceanDNA-b35988/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:11,661] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:11,662] [INFO] Task started: HMMsearch
[2023-03-17 05:35:11,662] [INFO] Running command: hmmsearch --tblout OceanDNA-b35988/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference/reference_markers.hmm OceanDNA-b35988/protein.faa > /dev/null
[2023-03-17 05:35:11,844] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:11,845] [INFO] Found 6/6 markers.
[2023-03-17 05:35:11,873] [INFO] Query marker FASTA was written to OceanDNA-b35988/markers.fasta
[2023-03-17 05:35:11,874] [INFO] Task started: Blastn
[2023-03-17 05:35:11,875] [INFO] Running command: blastn -query OceanDNA-b35988/markers.fasta -db /var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference/reference_markers.fasta -out OceanDNA-b35988/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:12,459] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:12,462] [INFO] Selected 33 target genomes.
[2023-03-17 05:35:12,462] [INFO] Target genome list was writen to OceanDNA-b35988/target_genomes.txt
[2023-03-17 05:35:12,482] [INFO] Task started: fastANI
[2023-03-17 05:35:12,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f6530f-bbb9-41c5-87b1-7d98b203cd73/OceanDNA-b35988.fa --refList OceanDNA-b35988/target_genomes.txt --output OceanDNA-b35988/fastani_result.tsv --threads 1
[2023-03-17 05:35:30,216] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:30,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:30,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:30,220] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:35:30,220] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:35:30,220] [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
Methyloprofundus sedimenti	strain=WF1	GCA_002072955.1	1420851	1420851	type	True	76.5807	59	747	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:35:30,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35988/tc_result.tsv
[2023-03-17 05:35:30,223] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:30,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:30,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference/checkm_data
[2023-03-17 05:35:30,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:30,292] [INFO] Task started: CheckM
[2023-03-17 05:35:30,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35988/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35988/checkm_input OceanDNA-b35988/checkm_result
[2023-03-17 05:36:04,641] [INFO] Task succeeded: CheckM
[2023-03-17 05:36:04,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:36:04,676] [INFO] ===== Completeness check finished =====
[2023-03-17 05:36:04,676] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:36:04,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35988/markers.fasta)
[2023-03-17 05:36:04,677] [INFO] Task started: Blastn
[2023-03-17 05:36:04,677] [INFO] Running command: blastn -query OceanDNA-b35988/markers.fasta -db /var/lib/cwl/stg39d33d5b-65e5-49af-bc68-7e8b1e267dac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35988/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:36:05,617] [INFO] Task succeeded: Blastn
[2023-03-17 05:36:05,623] [INFO] Selected 27 target genomes.
[2023-03-17 05:36:05,623] [INFO] Target genome list was writen to OceanDNA-b35988/target_genomes_gtdb.txt
[2023-03-17 05:36:05,799] [INFO] Task started: fastANI
[2023-03-17 05:36:05,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f6530f-bbb9-41c5-87b1-7d98b203cd73/OceanDNA-b35988.fa --refList OceanDNA-b35988/target_genomes_gtdb.txt --output OceanDNA-b35988/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:36:19,135] [INFO] Task succeeded: fastANI
[2023-03-17 05:36:19,140] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:36:19,140] [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_003666325.1	s__QPIN01 sp003666325	78.6308	255	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__QPIN01	95.0	99.86	99.86	0.96	0.96	2	-
GCA_003666385.1	s__QPIN01 sp003666385	78.6058	283	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__QPIN01	95.0	99.51	99.51	0.97	0.97	2	-
GCA_012960135.1	s__Methyloprofundus sp012960135	77.546	53	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	98.32	97.92	0.84	0.80	9	-
GCA_013139755.1	s__QPIN01 sp013139755	77.0355	131	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__QPIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002189065.1	s__Methyloprofundus sp002189065	76.9264	55	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016592635.1	s__Methyloprofundus sp016592635	76.7379	64	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128525.1	s__Methyloprofundus sp900128525	76.4554	53	747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:36:19,142] [INFO] GTDB search result was written to OceanDNA-b35988/result_gtdb.tsv
[2023-03-17 05:36:19,144] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:36:19,146] [INFO] DFAST_QC result json was written to OceanDNA-b35988/dqc_result.json
[2023-03-17 05:36:19,147] [INFO] DFAST_QC completed!
[2023-03-17 05:36:19,147] [INFO] Total running time: 0h1m21s