[2023-03-16 19:36:20,889] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:36:20,889] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:36:20,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference
[2023-03-16 19:36:23,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:36:23,388] [INFO] Task started: Prodigal
[2023-03-16 19:36:23,391] [INFO] Running command: cat /var/lib/cwl/stg2c4af0c9-98eb-40af-ad4a-340c566b7e55/OceanDNA-b42269.fa | prodigal -d OceanDNA-b42269/cds.fna -a OceanDNA-b42269/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:36:28,217] [INFO] Task succeeded: Prodigal
[2023-03-16 19:36:28,217] [INFO] Task started: HMMsearch
[2023-03-16 19:36:28,217] [INFO] Running command: hmmsearch --tblout OceanDNA-b42269/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference/reference_markers.hmm OceanDNA-b42269/protein.faa > /dev/null
[2023-03-16 19:36:28,350] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:36:28,350] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2c4af0c9-98eb-40af-ad4a-340c566b7e55/OceanDNA-b42269.fa]
[2023-03-16 19:36:28,357] [INFO] Query marker FASTA was written to OceanDNA-b42269/markers.fasta
[2023-03-16 19:36:28,358] [INFO] Task started: Blastn
[2023-03-16 19:36:28,358] [INFO] Running command: blastn -query OceanDNA-b42269/markers.fasta -db /var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference/reference_markers.fasta -out OceanDNA-b42269/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:36:28,855] [INFO] Task succeeded: Blastn
[2023-03-16 19:36:28,856] [INFO] Selected 6 target genomes.
[2023-03-16 19:36:28,856] [INFO] Target genome list was writen to OceanDNA-b42269/target_genomes.txt
[2023-03-16 19:36:28,863] [INFO] Task started: fastANI
[2023-03-16 19:36:28,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c4af0c9-98eb-40af-ad4a-340c566b7e55/OceanDNA-b42269.fa --refList OceanDNA-b42269/target_genomes.txt --output OceanDNA-b42269/fastani_result.tsv --threads 1
[2023-03-16 19:36:32,168] [INFO] Task succeeded: fastANI
[2023-03-16 19:36:32,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:36:32,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:36:32,169] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:36:32,169] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:36:32,169] [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
--------------------------------------------------------------------------------
[2023-03-16 19:36:32,169] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42269/tc_result.tsv
[2023-03-16 19:36:32,169] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:36:32,169] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:36:32,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference/checkm_data
[2023-03-16 19:36:32,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:36:32,344] [INFO] Task started: CheckM
[2023-03-16 19:36:32,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42269/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42269/checkm_input OceanDNA-b42269/checkm_result
[2023-03-16 19:36:48,541] [INFO] Task succeeded: CheckM
[2023-03-16 19:36:48,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:36:48,543] [INFO] ===== Completeness check finished =====
[2023-03-16 19:36:48,544] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:36:48,544] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42269/markers.fasta)
[2023-03-16 19:36:48,545] [INFO] Task started: Blastn
[2023-03-16 19:36:48,545] [INFO] Running command: blastn -query OceanDNA-b42269/markers.fasta -db /var/lib/cwl/stg1881a350-0c91-4a10-ae47-9f9e7c04a2b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42269/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:36:49,149] [INFO] Task succeeded: Blastn
[2023-03-16 19:36:49,150] [INFO] Selected 15 target genomes.
[2023-03-16 19:36:49,150] [INFO] Target genome list was writen to OceanDNA-b42269/target_genomes_gtdb.txt
[2023-03-16 19:36:49,164] [INFO] Task started: fastANI
[2023-03-16 19:36:49,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c4af0c9-98eb-40af-ad4a-340c566b7e55/OceanDNA-b42269.fa --refList OceanDNA-b42269/target_genomes_gtdb.txt --output OceanDNA-b42269/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:36:52,079] [INFO] Task succeeded: fastANI
[2023-03-16 19:36:52,087] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:36:52,087] [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_002169625.2	s__SAR86A sp002169625	98.7474	176	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	conclusive
GCA_902582355.1	s__SAR86A sp902582355	79.4465	85	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	-
GCA_902517505.1	s__SAR86A sp902517505	78.639	108	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902556105.1	s__SAR86A sp902556105	78.3278	93	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560315.1	s__SAR86A sp902560315	78.2778	114	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_002721465.1	s__SAR86A sp002721465	78.1521	61	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	-
GCA_902586925.1	s__SAR86A sp902586925	78.0257	110	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_902517425.1	s__SAR86A sp902517425	77.8826	76	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630885.1	s__SAR86A sp902630885	77.8284	89	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520495.1	s__SAR86A sp902520495	77.8197	90	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558095.1	s__SAR86A sp902558095	77.703	86	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528875.1	s__SAR86A sp902528875	77.5792	72	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	77.4079	75	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	77.0949	86	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-16 19:36:52,088] [INFO] GTDB search result was written to OceanDNA-b42269/result_gtdb.tsv
[2023-03-16 19:36:52,088] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:36:52,089] [INFO] DFAST_QC result json was written to OceanDNA-b42269/dqc_result.json
[2023-03-16 19:36:52,089] [INFO] DFAST_QC completed!
[2023-03-16 19:36:52,089] [INFO] Total running time: 0h0m31s