[2023-03-16 19:02:05,883] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:02:05,883] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:02:05,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference
[2023-03-16 19:02:07,707] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:02:07,708] [INFO] Task started: Prodigal
[2023-03-16 19:02:07,708] [INFO] Running command: cat /var/lib/cwl/stga229907c-b271-496b-bfc2-4f4af36fba12/OceanDNA-b16530.fa | prodigal -d OceanDNA-b16530/cds.fna -a OceanDNA-b16530/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:02:25,188] [INFO] Task succeeded: Prodigal
[2023-03-16 19:02:25,189] [INFO] Task started: HMMsearch
[2023-03-16 19:02:25,189] [INFO] Running command: hmmsearch --tblout OceanDNA-b16530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference/reference_markers.hmm OceanDNA-b16530/protein.faa > /dev/null
[2023-03-16 19:02:25,366] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:02:25,367] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga229907c-b271-496b-bfc2-4f4af36fba12/OceanDNA-b16530.fa]
[2023-03-16 19:02:25,379] [INFO] Query marker FASTA was written to OceanDNA-b16530/markers.fasta
[2023-03-16 19:02:25,380] [INFO] Task started: Blastn
[2023-03-16 19:02:25,380] [INFO] Running command: blastn -query OceanDNA-b16530/markers.fasta -db /var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference/reference_markers.fasta -out OceanDNA-b16530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:02:25,887] [INFO] Task succeeded: Blastn
[2023-03-16 19:02:25,888] [INFO] Selected 21 target genomes.
[2023-03-16 19:02:25,888] [INFO] Target genome list was writen to OceanDNA-b16530/target_genomes.txt
[2023-03-16 19:02:25,902] [INFO] Task started: fastANI
[2023-03-16 19:02:25,902] [INFO] Running command: fastANI --query /var/lib/cwl/stga229907c-b271-496b-bfc2-4f4af36fba12/OceanDNA-b16530.fa --refList OceanDNA-b16530/target_genomes.txt --output OceanDNA-b16530/fastani_result.tsv --threads 1
[2023-03-16 19:02:45,507] [INFO] Task succeeded: fastANI
[2023-03-16 19:02:45,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:02:45,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:02:45,510] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:02:45,510] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:02:45,511] [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	79.2027	307	455	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:02:45,511] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16530/tc_result.tsv
[2023-03-16 19:02:45,511] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:02:45,511] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:02:45,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference/checkm_data
[2023-03-16 19:02:45,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:02:45,797] [INFO] Task started: CheckM
[2023-03-16 19:02:45,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16530/checkm_input OceanDNA-b16530/checkm_result
[2023-03-16 19:03:28,665] [INFO] Task succeeded: CheckM
[2023-03-16 19:03:28,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.25%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 19:03:28,669] [INFO] ===== Completeness check finished =====
[2023-03-16 19:03:28,669] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:03:28,669] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16530/markers.fasta)
[2023-03-16 19:03:28,670] [INFO] Task started: Blastn
[2023-03-16 19:03:28,671] [INFO] Running command: blastn -query OceanDNA-b16530/markers.fasta -db /var/lib/cwl/stgb0c86ade-4a0c-43da-9b65-21443921a623/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:03:29,516] [INFO] Task succeeded: Blastn
[2023-03-16 19:03:29,517] [INFO] Selected 16 target genomes.
[2023-03-16 19:03:29,517] [INFO] Target genome list was writen to OceanDNA-b16530/target_genomes_gtdb.txt
[2023-03-16 19:03:29,549] [INFO] Task started: fastANI
[2023-03-16 19:03:29,549] [INFO] Running command: fastANI --query /var/lib/cwl/stga229907c-b271-496b-bfc2-4f4af36fba12/OceanDNA-b16530.fa --refList OceanDNA-b16530/target_genomes_gtdb.txt --output OceanDNA-b16530/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:03:36,330] [INFO] Task succeeded: fastANI
[2023-03-16 19:03:36,340] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:03:36,340] [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_003210735.1	s__Synechococcus_E sp003210735	80.6558	254	455	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.42	95.39	0.68	0.68	3	-
GCA_003210795.1	s__Synechococcus_E sp003210795	80.5525	250	455	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_003211235.1	s__Synechococcus_E sp003211235	80.5309	167	455	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_014279895.1	s__Synechococcus_E sp002724845	79.6161	285	455	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_014280175.1	s__Synechococcus_E sp004212765	79.5179	300	455	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_000737595.1	s__Synechococcus_E sp000737595	79.4985	263	455	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_000161795.2	s__Synechococcus_E sp000161795	79.4969	269	455	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	79.2125	227	455	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_014280195.1	s__Synechococcus_E sp014280195	79.1907	295	455	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_016779825.1	s__Synechococcus_E sp016779825	79.1296	220	455	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_000737575.1	s__Synechococcus_E sp000737575	78.8982	270	455	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	-
GCA_003211535.1	s__Synechococcus_E sp003211535	78.5861	217	455	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_002691345.1	s__Synechococcus_E sp002691345	78.3759	202	455	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_002252675.1	s__Cyanobium sp002252675	77.7126	169	455	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCF_004209775.1	s__Synechococcus_C sp004209775	77.6895	216	455	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903934375.1	s__Vulcanococcus sp903934375	77.657	145	455	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.96	98.94	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-16 19:03:36,341] [INFO] GTDB search result was written to OceanDNA-b16530/result_gtdb.tsv
[2023-03-16 19:03:36,341] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:03:36,343] [INFO] DFAST_QC result json was written to OceanDNA-b16530/dqc_result.json
[2023-03-16 19:03:36,343] [INFO] DFAST_QC completed!
[2023-03-16 19:03:36,343] [INFO] Total running time: 0h1m30s