[2023-03-17 04:48:53,954] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,155] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,155] [INFO] Running command: cat /var/lib/cwl/stg9aed476e-76f3-48c1-b18c-4e269a723c09/OceanDNA-b15515.fa | prodigal -d OceanDNA-b15515/cds.fna -a OceanDNA-b15515/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:16,739] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:16,740] [INFO] Task started: HMMsearch
[2023-03-17 04:49:16,740] [INFO] Running command: hmmsearch --tblout OceanDNA-b15515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference/reference_markers.hmm OceanDNA-b15515/protein.faa > /dev/null
[2023-03-17 04:49:16,934] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:16,935] [INFO] Found 6/6 markers.
[2023-03-17 04:49:16,955] [INFO] Query marker FASTA was written to OceanDNA-b15515/markers.fasta
[2023-03-17 04:49:16,955] [INFO] Task started: Blastn
[2023-03-17 04:49:16,955] [INFO] Running command: blastn -query OceanDNA-b15515/markers.fasta -db /var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference/reference_markers.fasta -out OceanDNA-b15515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:17,467] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:17,468] [INFO] Selected 21 target genomes.
[2023-03-17 04:49:17,468] [INFO] Target genome list was writen to OceanDNA-b15515/target_genomes.txt
[2023-03-17 04:49:17,479] [INFO] Task started: fastANI
[2023-03-17 04:49:17,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aed476e-76f3-48c1-b18c-4e269a723c09/OceanDNA-b15515.fa --refList OceanDNA-b15515/target_genomes.txt --output OceanDNA-b15515/fastani_result.tsv --threads 1
[2023-03-17 04:49:35,576] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:35,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:35,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:35,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:35,577] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:35,577] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:35,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15515/tc_result.tsv
[2023-03-17 04:49:35,577] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:35,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:35,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference/checkm_data
[2023-03-17 04:49:35,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:35,585] [INFO] Task started: CheckM
[2023-03-17 04:49:35,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15515/checkm_input OceanDNA-b15515/checkm_result
[2023-03-17 04:50:28,802] [INFO] Task succeeded: CheckM
[2023-03-17 04:50:28,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:50:28,804] [INFO] ===== Completeness check finished =====
[2023-03-17 04:50:28,805] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:50:28,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15515/markers.fasta)
[2023-03-17 04:50:28,805] [INFO] Task started: Blastn
[2023-03-17 04:50:28,805] [INFO] Running command: blastn -query OceanDNA-b15515/markers.fasta -db /var/lib/cwl/stgba988024-aa36-44c8-939f-4b1b09cbac3e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:50:29,535] [INFO] Task succeeded: Blastn
[2023-03-17 04:50:29,536] [INFO] Selected 22 target genomes.
[2023-03-17 04:50:29,536] [INFO] Target genome list was writen to OceanDNA-b15515/target_genomes_gtdb.txt
[2023-03-17 04:50:30,248] [INFO] Task started: fastANI
[2023-03-17 04:50:30,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aed476e-76f3-48c1-b18c-4e269a723c09/OceanDNA-b15515.fa --refList OceanDNA-b15515/target_genomes_gtdb.txt --output OceanDNA-b15515/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:40,929] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:40,936] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:50:40,936] [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_002816875.1	s__Io17-Chloro-G2 sp002816875	99.8378	475	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Io17-Chloro-G2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002721995.1	s__UBA9611 sp002721995	76.4655	134	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_009692925.1	s__SHYG01 sp009692925	76.2705	127	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_002328185.1	s__UBA9611 sp002328185	76.2504	130	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_009840175.1	s__VXOI01 sp009840175	76.2072	108	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
GCA_002816575.1	s__UBA9611 sp002816575	76.0641	115	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837355.1	s__Bin87 sp009837355	75.9801	106	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	99.97	99.97	0.97	0.97	2	-
GCA_013204585.1	s__UBA9611 sp013204585	75.9437	89	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392095.1	s__UBA9611 sp009391975	75.9293	101	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_009392075.1	s__UBA9611 sp009392075	75.8852	65	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_002746355.1	s__UBA9611 sp002746355	75.7374	130	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002698265.1	s__UBA9611 sp002698265	75.7285	84	1136	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:40,936] [INFO] GTDB search result was written to OceanDNA-b15515/result_gtdb.tsv
[2023-03-17 04:50:40,936] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:40,937] [INFO] DFAST_QC result json was written to OceanDNA-b15515/dqc_result.json
[2023-03-17 04:50:40,937] [INFO] DFAST_QC completed!
[2023-03-17 04:50:40,938] [INFO] Total running time: 0h1m47s