[2023-03-15 03:25:37,019] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:25:37,019] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:25:37,020] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference
[2023-03-15 03:25:38,182] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:25:38,183] [INFO] Task started: Prodigal
[2023-03-15 03:25:38,183] [INFO] Running command: cat /var/lib/cwl/stgadd58d1c-c085-4589-8ccf-e52e70d2cbea/OceanDNA-b16674.fa | prodigal -d OceanDNA-b16674/cds.fna -a OceanDNA-b16674/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:25:55,126] [INFO] Task succeeded: Prodigal
[2023-03-15 03:25:55,126] [INFO] Task started: HMMsearch
[2023-03-15 03:25:55,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b16674/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference/reference_markers.hmm OceanDNA-b16674/protein.faa > /dev/null
[2023-03-15 03:25:55,296] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:25:55,297] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgadd58d1c-c085-4589-8ccf-e52e70d2cbea/OceanDNA-b16674.fa]
[2023-03-15 03:25:55,311] [INFO] Query marker FASTA was written to OceanDNA-b16674/markers.fasta
[2023-03-15 03:25:55,312] [INFO] Task started: Blastn
[2023-03-15 03:25:55,312] [INFO] Running command: blastn -query OceanDNA-b16674/markers.fasta -db /var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference/reference_markers.fasta -out OceanDNA-b16674/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:25:55,825] [INFO] Task succeeded: Blastn
[2023-03-15 03:25:55,826] [INFO] Selected 20 target genomes.
[2023-03-15 03:25:55,826] [INFO] Target genome list was writen to OceanDNA-b16674/target_genomes.txt
[2023-03-15 03:25:55,838] [INFO] Task started: fastANI
[2023-03-15 03:25:55,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgadd58d1c-c085-4589-8ccf-e52e70d2cbea/OceanDNA-b16674.fa --refList OceanDNA-b16674/target_genomes.txt --output OceanDNA-b16674/fastani_result.tsv --threads 1
[2023-03-15 03:26:08,748] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:08,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:26:08,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:26:08,752] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:26:08,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:26:08,752] [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	77.2776	114	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:26:08,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16674/tc_result.tsv
[2023-03-15 03:26:08,752] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:26:08,753] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:26:08,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference/checkm_data
[2023-03-15 03:26:08,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:26:08,757] [INFO] Task started: CheckM
[2023-03-15 03:26:08,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16674/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16674/checkm_input OceanDNA-b16674/checkm_result
[2023-03-15 03:26:55,232] [INFO] Task succeeded: CheckM
[2023-03-15 03:26:55,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:26:55,234] [INFO] ===== Completeness check finished =====
[2023-03-15 03:26:55,234] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:26:55,234] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16674/markers.fasta)
[2023-03-15 03:26:55,235] [INFO] Task started: Blastn
[2023-03-15 03:26:55,236] [INFO] Running command: blastn -query OceanDNA-b16674/markers.fasta -db /var/lib/cwl/stgcd548c18-827b-4f2c-8e81-181107e71f3b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16674/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:26:56,002] [INFO] Task succeeded: Blastn
[2023-03-15 03:26:56,003] [INFO] Selected 21 target genomes.
[2023-03-15 03:26:56,003] [INFO] Target genome list was writen to OceanDNA-b16674/target_genomes_gtdb.txt
[2023-03-15 03:26:56,047] [INFO] Task started: fastANI
[2023-03-15 03:26:56,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgadd58d1c-c085-4589-8ccf-e52e70d2cbea/OceanDNA-b16674.fa --refList OceanDNA-b16674/target_genomes_gtdb.txt --output OceanDNA-b16674/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:27:04,058] [INFO] Task succeeded: fastANI
[2023-03-15 03:27:04,069] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:27:04,070] [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_002701375.1	s__Synechococcus_E sp002701375	99.7025	563	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	99.66	99.66	0.75	0.75	2	conclusive
GCA_003211515.1	s__Synechococcus_E sp003211515	78.2768	103	641	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	77.3752	81	641	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_014279895.1	s__Synechococcus_E sp002724845	77.2546	110	641	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	77.2539	113	641	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_014279755.1	s__Synechococcus_E sp014279755	77.2051	112	641	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	77.1665	93	641	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_002700765.1	s__Synechococcus_E sp002700765	77.1577	100	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000737535.1	s__Synechococcus_E sp000737535	77.1498	131	641	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_014279875.1	s__Synechococcus_C sp002172935	76.9818	74	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.09	98.09	0.93	0.93	2	-
GCA_016779825.1	s__Synechococcus_E sp016779825	76.9362	79	641	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_000012505.1	s__Synechococcus_E sp000012505	76.93	83	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.61	95.06	0.95	0.89	4	-
GCA_002170825.1	s__Synechococcus_E sp002170825	76.6995	67	641	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	-
GCF_000515235.1	s__Synechococcus_E sp000515235	76.6989	130	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	97.70	97.70	0.82	0.82	2	-
GCA_000063505.1	s__Synechococcus_C sp000063505	76.6305	67	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.52	97.52	0.89	0.89	2	-
GCF_014279795.1	s__Synechococcus_C sp014279795	76.6119	74	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.67	96.56	0.92	0.91	3	-
GCF_014280235.1	s__NIES-981 sp014280235	76.38	53	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	97.33	97.33	0.87	0.87	2	-
GCF_000230675.1	s__Synechococcus_C sp000230675	76.3578	66	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.29	95.09	0.90	0.84	8	-
GCF_014279775.1	s__Synechococcus_C sp002500205	76.0022	60	641	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.03	97.76	0.95	0.86	9	-
--------------------------------------------------------------------------------
[2023-03-15 03:27:04,070] [INFO] GTDB search result was written to OceanDNA-b16674/result_gtdb.tsv
[2023-03-15 03:27:04,070] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:27:04,071] [INFO] DFAST_QC result json was written to OceanDNA-b16674/dqc_result.json
[2023-03-15 03:27:04,071] [INFO] DFAST_QC completed!
[2023-03-15 03:27:04,071] [INFO] Total running time: 0h1m27s