[2023-03-17 14:51:39,394] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:51:39,395] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:51:39,395] [INFO] DQC Reference Directory: /var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference
[2023-03-17 14:51:40,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:51:40,529] [INFO] Task started: Prodigal
[2023-03-17 14:51:40,529] [INFO] Running command: cat /var/lib/cwl/stg0179f6bb-7020-402d-9843-d5e584573e1f/OceanDNA-b43282.fa | prodigal -d OceanDNA-b43282/cds.fna -a OceanDNA-b43282/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:51:45,543] [INFO] Task succeeded: Prodigal
[2023-03-17 14:51:45,543] [INFO] Task started: HMMsearch
[2023-03-17 14:51:45,543] [INFO] Running command: hmmsearch --tblout OceanDNA-b43282/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference/reference_markers.hmm OceanDNA-b43282/protein.faa > /dev/null
[2023-03-17 14:51:45,712] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:51:45,712] [INFO] Found 6/6 markers.
[2023-03-17 14:51:45,721] [INFO] Query marker FASTA was written to OceanDNA-b43282/markers.fasta
[2023-03-17 14:51:45,722] [INFO] Task started: Blastn
[2023-03-17 14:51:45,722] [INFO] Running command: blastn -query OceanDNA-b43282/markers.fasta -db /var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference/reference_markers.fasta -out OceanDNA-b43282/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:51:46,321] [INFO] Task succeeded: Blastn
[2023-03-17 14:51:46,322] [INFO] Selected 27 target genomes.
[2023-03-17 14:51:46,323] [INFO] Target genome list was writen to OceanDNA-b43282/target_genomes.txt
[2023-03-17 14:51:46,339] [INFO] Task started: fastANI
[2023-03-17 14:51:46,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg0179f6bb-7020-402d-9843-d5e584573e1f/OceanDNA-b43282.fa --refList OceanDNA-b43282/target_genomes.txt --output OceanDNA-b43282/fastani_result.tsv --threads 1
[2023-03-17 14:52:07,608] [INFO] Task succeeded: fastANI
[2023-03-17 14:52:07,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:52:07,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:52:07,612] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:52:07,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:52:07,612] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	82.2667	253	300	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:52:07,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43282/tc_result.tsv
[2023-03-17 14:52:07,612] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:52:07,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:52:07,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference/checkm_data
[2023-03-17 14:52:07,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:52:07,615] [INFO] Task started: CheckM
[2023-03-17 14:52:07,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43282/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43282/checkm_input OceanDNA-b43282/checkm_result
[2023-03-17 14:52:30,140] [INFO] Task succeeded: CheckM
[2023-03-17 14:52:30,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:52:30,149] [INFO] ===== Completeness check finished =====
[2023-03-17 14:52:30,149] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:52:30,149] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43282/markers.fasta)
[2023-03-17 14:52:30,149] [INFO] Task started: Blastn
[2023-03-17 14:52:30,149] [INFO] Running command: blastn -query OceanDNA-b43282/markers.fasta -db /var/lib/cwl/stga88c2102-7b4a-4597-8719-5fdd65ec12a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43282/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:52:31,162] [INFO] Task succeeded: Blastn
[2023-03-17 14:52:31,162] [INFO] Selected 13 target genomes.
[2023-03-17 14:52:31,163] [INFO] Target genome list was writen to OceanDNA-b43282/target_genomes_gtdb.txt
[2023-03-17 14:52:31,297] [INFO] Task started: fastANI
[2023-03-17 14:52:31,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg0179f6bb-7020-402d-9843-d5e584573e1f/OceanDNA-b43282.fa --refList OceanDNA-b43282/target_genomes_gtdb.txt --output OceanDNA-b43282/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:52:38,253] [INFO] Task succeeded: fastANI
[2023-03-17 14:52:38,262] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 14:52:38,263] [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_001293165.1	s__Thioglobus autotrophicus	82.2667	253	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018644675.1	s__Thioglobus sp018644675	80.7517	229	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.74	99.56	0.96	0.91	16	-
GCF_900128515.1	s__Thioglobus sp900128515	79.6853	174	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.64	99.26	0.90	0.80	8	-
GCA_014384345.1	s__Thioglobus pontius	79.6482	182	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCA_900180385.1	s__Thioglobus sp900180385	79.425	193	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963715.1	s__Thioglobus sp012963715	79.1884	138	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	97.05	95.18	0.84	0.80	5	-
GCA_018648985.1	s__UBA2013 sp018648985	77.7103	101	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128535.1	s__Thiodubiliella sp900128535	77.6951	80	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.14	96.23	0.87	0.79	15	-
GCF_003711265.1	s__Thiodubiliella sp001875585	77.5619	78	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.68	98.49	0.94	0.89	5	-
GCA_012963565.1	s__DTVJ01 sp012963565	77.4562	69	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547755.1	s__Thiodubiliella sp001547755	77.3948	76	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.63	98.63	0.76	0.76	2	-
GCA_003978285.1	s__UBA2013 sp003978285	77.2808	71	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:52:38,263] [INFO] GTDB search result was written to OceanDNA-b43282/result_gtdb.tsv
[2023-03-17 14:52:38,263] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:52:38,264] [INFO] DFAST_QC result json was written to OceanDNA-b43282/dqc_result.json
[2023-03-17 14:52:38,264] [INFO] DFAST_QC completed!
[2023-03-17 14:52:38,264] [INFO] Total running time: 0h0m59s