[2023-03-18 07:06:20,049] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference
[2023-03-18 07:06:21,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,162] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,162] [INFO] Running command: cat /var/lib/cwl/stgab6d3f81-36bb-43f9-9abb-038bb4525c3e/OceanDNA-b16622.fa | prodigal -d OceanDNA-b16622/cds.fna -a OceanDNA-b16622/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:38,226] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:38,226] [INFO] Task started: HMMsearch
[2023-03-18 07:06:38,226] [INFO] Running command: hmmsearch --tblout OceanDNA-b16622/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference/reference_markers.hmm OceanDNA-b16622/protein.faa > /dev/null
[2023-03-18 07:06:38,399] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:38,399] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab6d3f81-36bb-43f9-9abb-038bb4525c3e/OceanDNA-b16622.fa]
[2023-03-18 07:06:38,413] [INFO] Query marker FASTA was written to OceanDNA-b16622/markers.fasta
[2023-03-18 07:06:38,413] [INFO] Task started: Blastn
[2023-03-18 07:06:38,413] [INFO] Running command: blastn -query OceanDNA-b16622/markers.fasta -db /var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference/reference_markers.fasta -out OceanDNA-b16622/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:38,939] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:38,940] [INFO] Selected 21 target genomes.
[2023-03-18 07:06:38,941] [INFO] Target genome list was writen to OceanDNA-b16622/target_genomes.txt
[2023-03-18 07:06:38,952] [INFO] Task started: fastANI
[2023-03-18 07:06:38,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgab6d3f81-36bb-43f9-9abb-038bb4525c3e/OceanDNA-b16622.fa --refList OceanDNA-b16622/target_genomes.txt --output OceanDNA-b16622/fastani_result.tsv --threads 1
[2023-03-18 07:06:52,532] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:52,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:52,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:52,536] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:52,536] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:52,536] [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	80.5489	398	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:52,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16622/tc_result.tsv
[2023-03-18 07:06:52,536] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:52,536] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:52,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference/checkm_data
[2023-03-18 07:06:52,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:52,541] [INFO] Task started: CheckM
[2023-03-18 07:06:52,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16622/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16622/checkm_input OceanDNA-b16622/checkm_result
[2023-03-18 07:07:42,866] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:42,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:42,868] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:42,868] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:42,869] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16622/markers.fasta)
[2023-03-18 07:07:42,869] [INFO] Task started: Blastn
[2023-03-18 07:07:42,869] [INFO] Running command: blastn -query OceanDNA-b16622/markers.fasta -db /var/lib/cwl/stg17fbaf8c-e1c2-4445-b640-62d36b41b157/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16622/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:43,673] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:43,674] [INFO] Selected 19 target genomes.
[2023-03-18 07:07:43,674] [INFO] Target genome list was writen to OceanDNA-b16622/target_genomes_gtdb.txt
[2023-03-18 07:07:43,951] [INFO] Task started: fastANI
[2023-03-18 07:07:43,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgab6d3f81-36bb-43f9-9abb-038bb4525c3e/OceanDNA-b16622.fa --refList OceanDNA-b16622/target_genomes_gtdb.txt --output OceanDNA-b16622/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:52,095] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:52,106] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:07:52,106] [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_000737575.1	s__Synechococcus_E sp000737575	98.929	633	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.69	96.21	0.96	0.90	8	conclusive
GCF_014280175.1	s__Synechococcus_E sp004212765	80.7203	409	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
GCF_014280195.1	s__Synechococcus_E sp014280195	80.5771	392	648	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_000195975.1	s__Synechococcus_E sp000195975	80.5489	398	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCF_014279895.1	s__Synechococcus_E sp002724845	80.2653	359	648	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	80.0493	336	648	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	79.908	350	648	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_014279755.1	s__Synechococcus_E sp014279755	79.8783	342	648	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	-
GCA_013911515.1	s__Synechococcus_E sp013911515	79.8776	294	648	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	-
GCA_002170825.1	s__Synechococcus_E sp002170825	79.7508	219	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCA_016882415.1	s__Vulcanococcus sp016882415	79.4895	159	648	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_900474185.1	s__Synechococcus_E sp900474185	79.3544	353	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.68	95.24	0.90	0.90	3	-
GCA_002691345.1	s__Synechococcus_E sp002691345	79.2876	247	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.96	0.96	2	-
GCF_019038415.1	s__Cyanobium sp019038415	78.8353	253	648	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_003003925.1	s__Cyanobium minutissimum	78.6609	283	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCA_007694915.1	s__NIES-981 sp007694915	78.566	256	648	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	-
GCA_903934375.1	s__Vulcanococcus sp903934375	78.5477	222	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.96	98.94	0.87	0.87	3	-
GCF_001039265.1	s__NIES-981 sp001039265	78.5416	212	648	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	-
GCA_903882285.1	s__Cyanobium sp903882285	78.1112	230	648	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.61	99.61	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:52,106] [INFO] GTDB search result was written to OceanDNA-b16622/result_gtdb.tsv
[2023-03-18 07:07:52,106] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:52,108] [INFO] DFAST_QC result json was written to OceanDNA-b16622/dqc_result.json
[2023-03-18 07:07:52,108] [INFO] DFAST_QC completed!
[2023-03-18 07:07:52,108] [INFO] Total running time: 0h1m32s