[2023-03-19 00:01:03,287] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,288] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,288] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference
[2023-03-19 00:01:04,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,577] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,577] [INFO] Running command: cat /var/lib/cwl/stgf33dc550-186b-40fe-8e4c-74e4b667f657/OceanDNA-b16463.fa | prodigal -d OceanDNA-b16463/cds.fna -a OceanDNA-b16463/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:22,308] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:22,309] [INFO] Task started: HMMsearch
[2023-03-19 00:01:22,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b16463/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference/reference_markers.hmm OceanDNA-b16463/protein.faa > /dev/null
[2023-03-19 00:01:22,543] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:22,543] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf33dc550-186b-40fe-8e4c-74e4b667f657/OceanDNA-b16463.fa]
[2023-03-19 00:01:22,557] [INFO] Query marker FASTA was written to OceanDNA-b16463/markers.fasta
[2023-03-19 00:01:22,557] [INFO] Task started: Blastn
[2023-03-19 00:01:22,557] [INFO] Running command: blastn -query OceanDNA-b16463/markers.fasta -db /var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference/reference_markers.fasta -out OceanDNA-b16463/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:23,092] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:23,093] [INFO] Selected 22 target genomes.
[2023-03-19 00:01:23,093] [INFO] Target genome list was writen to OceanDNA-b16463/target_genomes.txt
[2023-03-19 00:01:23,105] [INFO] Task started: fastANI
[2023-03-19 00:01:23,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgf33dc550-186b-40fe-8e4c-74e4b667f657/OceanDNA-b16463.fa --refList OceanDNA-b16463/target_genomes.txt --output OceanDNA-b16463/fastani_result.tsv --threads 1
[2023-03-19 00:01:38,780] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:38,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:38,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:38,784] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:38,784] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:38,784] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.7355	207	625	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	76.9421	104	625	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:38,784] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16463/tc_result.tsv
[2023-03-19 00:01:38,784] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:38,785] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:38,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference/checkm_data
[2023-03-19 00:01:38,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:38,793] [INFO] Task started: CheckM
[2023-03-19 00:01:38,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16463/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16463/checkm_input OceanDNA-b16463/checkm_result
[2023-03-19 00:02:26,897] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:26,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:26,900] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:26,900] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:26,900] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16463/markers.fasta)
[2023-03-19 00:02:26,901] [INFO] Task started: Blastn
[2023-03-19 00:02:26,901] [INFO] Running command: blastn -query OceanDNA-b16463/markers.fasta -db /var/lib/cwl/stgc7f0e1f4-c5a2-48e3-a4ff-d02c04e440b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16463/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:27,678] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:27,678] [INFO] Selected 17 target genomes.
[2023-03-19 00:02:27,678] [INFO] Target genome list was writen to OceanDNA-b16463/target_genomes_gtdb.txt
[2023-03-19 00:02:27,733] [INFO] Task started: fastANI
[2023-03-19 00:02:27,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgf33dc550-186b-40fe-8e4c-74e4b667f657/OceanDNA-b16463.fa --refList OceanDNA-b16463/target_genomes_gtdb.txt --output OceanDNA-b16463/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:35,504] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:35,514] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:35,514] [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_002470305.1	s__RCC307 sp002470305	99.4393	486	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.70	97.75	0.84	0.76	3	conclusive
GCA_002168155.1	s__RCC307 sp002168155	82.4129	477	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000063525.1	s__RCC307 sp000063525	79.9086	382	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.48	97.86	0.96	0.93	5	-
GCA_012270465.1	s__RCC307 sp012270465	79.6403	275	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.23	98.23	0.84	0.84	2	-
GCF_019038465.1	s__Cyanobium sp019038465	78.4719	240	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694915.1	s__NIES-981 sp007694915	78.4212	250	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038415.1	s__Cyanobium sp019038415	78.3895	247	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252675.1	s__Cyanobium sp002252675	78.3526	261	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCA_903943975.1	s__Synechococcus_D lacustris_A	78.3267	263	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	99.87	99.37	0.98	0.92	31	-
GCF_000155635.1	s__NIES-981 sp000155635	78.2492	260	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015841355.1	s__WH-5701 sp015841355	78.1342	244	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039265.1	s__NIES-981 sp001039265	78.1187	199	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015840715.1	s__Cyanobium sp015840715	77.9896	262	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029175.1	s__Vulcanococcus sp010029175	77.9331	205	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279895.1	s__Synechococcus_E sp002724845	77.8784	200	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCF_000161795.2	s__Synechococcus_E sp000161795	77.6804	186	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737595.1	s__Synechococcus_E sp000737595	77.651	189	625	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:35,514] [INFO] GTDB search result was written to OceanDNA-b16463/result_gtdb.tsv
[2023-03-19 00:02:35,514] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:35,516] [INFO] DFAST_QC result json was written to OceanDNA-b16463/dqc_result.json
[2023-03-19 00:02:35,516] [INFO] DFAST_QC completed!
[2023-03-19 00:02:35,516] [INFO] Total running time: 0h1m32s