[2023-03-18 21:53:45,255] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:53:45,255] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:53:45,255] [INFO] DQC Reference Directory: /var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference
[2023-03-18 21:53:47,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:53:47,072] [INFO] Task started: Prodigal
[2023-03-18 21:53:47,072] [INFO] Running command: cat /var/lib/cwl/stg101dd6e0-9053-481b-9f47-f2b6fc0996ba/OceanDNA-b25476.fa | prodigal -d OceanDNA-b25476/cds.fna -a OceanDNA-b25476/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:53:50,567] [INFO] Task succeeded: Prodigal
[2023-03-18 21:53:50,568] [INFO] Task started: HMMsearch
[2023-03-18 21:53:50,568] [INFO] Running command: hmmsearch --tblout OceanDNA-b25476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference/reference_markers.hmm OceanDNA-b25476/protein.faa > /dev/null
[2023-03-18 21:53:50,705] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:53:50,705] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg101dd6e0-9053-481b-9f47-f2b6fc0996ba/OceanDNA-b25476.fa]
[2023-03-18 21:53:50,714] [INFO] Query marker FASTA was written to OceanDNA-b25476/markers.fasta
[2023-03-18 21:53:50,715] [INFO] Task started: Blastn
[2023-03-18 21:53:50,715] [INFO] Running command: blastn -query OceanDNA-b25476/markers.fasta -db /var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference/reference_markers.fasta -out OceanDNA-b25476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:53:51,306] [INFO] Task succeeded: Blastn
[2023-03-18 21:53:51,307] [INFO] Selected 12 target genomes.
[2023-03-18 21:53:51,308] [INFO] Target genome list was writen to OceanDNA-b25476/target_genomes.txt
[2023-03-18 21:53:51,316] [INFO] Task started: fastANI
[2023-03-18 21:53:51,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg101dd6e0-9053-481b-9f47-f2b6fc0996ba/OceanDNA-b25476.fa --refList OceanDNA-b25476/target_genomes.txt --output OceanDNA-b25476/fastani_result.tsv --threads 1
[2023-03-18 21:53:55,003] [INFO] Task succeeded: fastANI
[2023-03-18 21:53:55,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:53:55,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:53:55,004] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:53:55,004] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:53:55,004] [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 21:53:55,005] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25476/tc_result.tsv
[2023-03-18 21:53:55,005] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:53:55,005] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:53:55,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference/checkm_data
[2023-03-18 21:53:55,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:53:55,019] [INFO] Task started: CheckM
[2023-03-18 21:53:55,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25476/checkm_input OceanDNA-b25476/checkm_result
[2023-03-18 21:54:13,655] [INFO] Task succeeded: CheckM
[2023-03-18 21:54:13,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 9.23%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:54:13,683] [INFO] ===== Completeness check finished =====
[2023-03-18 21:54:13,683] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:54:13,683] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25476/markers.fasta)
[2023-03-18 21:54:13,685] [INFO] Task started: Blastn
[2023-03-18 21:54:13,685] [INFO] Running command: blastn -query OceanDNA-b25476/markers.fasta -db /var/lib/cwl/stga0a299e5-f315-481b-ae8b-bbe2b3c8f6c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:54:14,673] [INFO] Task succeeded: Blastn
[2023-03-18 21:54:14,676] [INFO] Selected 14 target genomes.
[2023-03-18 21:54:14,676] [INFO] Target genome list was writen to OceanDNA-b25476/target_genomes_gtdb.txt
[2023-03-18 21:54:14,695] [INFO] Task started: fastANI
[2023-03-18 21:54:14,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg101dd6e0-9053-481b-9f47-f2b6fc0996ba/OceanDNA-b25476.fa --refList OceanDNA-b25476/target_genomes_gtdb.txt --output OceanDNA-b25476/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:54:17,484] [INFO] Task succeeded: fastANI
[2023-03-18 21:54:17,489] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:54:17,489] [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_008638005.1	s__HIMB114 sp008638005	97.0969	125	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002171085.1	s__HIMB114 sp002171085	79.7265	65	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.62	99.25	0.83	0.70	3	-
GCA_000163555.2	s__HIMB114 sp000163555	79.6889	95	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524955.1	s__HIMB114 sp902524955	77.7909	67	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684895.1	s__HIMB114 sp002684895	77.4352	61	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	97.17	97.17	0.86	0.86	2	-
GCA_002692055.1	s__HIMB114 sp002692055	77.3678	50	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.96	99.96	0.77	0.77	2	-
GCA_003209195.1	s__HIMB114 sp003209195	77.3303	51	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.64	99.28	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:54:17,490] [INFO] GTDB search result was written to OceanDNA-b25476/result_gtdb.tsv
[2023-03-18 21:54:17,493] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:54:17,494] [INFO] DFAST_QC result json was written to OceanDNA-b25476/dqc_result.json
[2023-03-18 21:54:17,495] [INFO] DFAST_QC completed!
[2023-03-18 21:54:17,495] [INFO] Total running time: 0h0m32s