[2023-03-15 17:24:01,320] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,321] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference
[2023-03-15 17:24:02,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,534] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,534] [INFO] Running command: cat /var/lib/cwl/stg8d93a65d-fa52-405e-82c2-b840b98dd3ad/OceanDNA-b16719.fa | prodigal -d OceanDNA-b16719/cds.fna -a OceanDNA-b16719/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:27,160] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:27,160] [INFO] Task started: HMMsearch
[2023-03-15 17:24:27,160] [INFO] Running command: hmmsearch --tblout OceanDNA-b16719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference/reference_markers.hmm OceanDNA-b16719/protein.faa > /dev/null
[2023-03-15 17:24:27,489] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:27,489] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8d93a65d-fa52-405e-82c2-b840b98dd3ad/OceanDNA-b16719.fa]
[2023-03-15 17:24:27,560] [INFO] Query marker FASTA was written to OceanDNA-b16719/markers.fasta
[2023-03-15 17:24:27,560] [INFO] Task started: Blastn
[2023-03-15 17:24:27,560] [INFO] Running command: blastn -query OceanDNA-b16719/markers.fasta -db /var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference/reference_markers.fasta -out OceanDNA-b16719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:28,108] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:28,109] [INFO] Selected 22 target genomes.
[2023-03-15 17:24:28,109] [INFO] Target genome list was writen to OceanDNA-b16719/target_genomes.txt
[2023-03-15 17:24:28,125] [INFO] Task started: fastANI
[2023-03-15 17:24:28,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d93a65d-fa52-405e-82c2-b840b98dd3ad/OceanDNA-b16719.fa --refList OceanDNA-b16719/target_genomes.txt --output OceanDNA-b16719/fastani_result.tsv --threads 1
[2023-03-15 17:24:41,479] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:41,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:41,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:41,485] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:41,485] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:24:41,485] [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	77.8816	220	856	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	76.7444	86	856	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.0279	52	856	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	74.7638	52	856	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	74.7637	58	856	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:41,485] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16719/tc_result.tsv
[2023-03-15 17:24:41,485] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:41,485] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:41,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference/checkm_data
[2023-03-15 17:24:41,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:41,490] [INFO] Task started: CheckM
[2023-03-15 17:24:41,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16719/checkm_input OceanDNA-b16719/checkm_result
[2023-03-15 17:25:45,412] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:45,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:45,415] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:45,415] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:45,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16719/markers.fasta)
[2023-03-15 17:25:45,416] [INFO] Task started: Blastn
[2023-03-15 17:25:45,416] [INFO] Running command: blastn -query OceanDNA-b16719/markers.fasta -db /var/lib/cwl/stg5a2b06fa-a284-45de-aeb2-c30f88183478/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:46,310] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:46,310] [INFO] Selected 18 target genomes.
[2023-03-15 17:25:46,311] [INFO] Target genome list was writen to OceanDNA-b16719/target_genomes_gtdb.txt
[2023-03-15 17:25:46,325] [INFO] Task started: fastANI
[2023-03-15 17:25:46,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d93a65d-fa52-405e-82c2-b840b98dd3ad/OceanDNA-b16719.fa --refList OceanDNA-b16719/target_genomes_gtdb.txt --output OceanDNA-b16719/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:25:57,111] [INFO] Task succeeded: fastANI
[2023-03-15 17:25:57,121] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:25:57,121] [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_002252635.1	s__MW101C3 sp002252635	89.9905	681	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__MW101C3	95.0	97.20	97.20	0.89	0.89	2	-
GCA_003249115.1	s__QBMD01 sp003249115	81.5298	480	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
GCF_014224355.1	s__WH-5701 sp014224355	80.8967	484	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015841355.1	s__WH-5701 sp015841355	80.889	525	856	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_000153045.1	s__WH-5701 sp000153045	80.8208	511	856	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_003003925.1	s__Cyanobium minutissimum	80.7388	507	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCF_002252675.1	s__Cyanobium sp002252675	80.731	498	856	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_002252625.1	s__WH-5701 sp002252625	80.6348	505	856	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_014698445.1	s__Cyanobium elabens	80.5724	527	856	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_016882315.1	s__Cyanobium sp016882315	80.5336	509	856	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_018399015.1	s__NIES-981 sp018399015	80.5126	501	856	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	80.4337	460	856	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_019038465.1	s__Cyanobium sp019038465	80.3934	483	856	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	80.2298	452	856	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_007135755.1	s__NIES-981 sp007135755	80.2055	442	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.54	99.54	0.92	0.92	2	-
GCA_010030955.1	s__Vulcanococcus sp010030955	79.6299	315	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.81	98.81	0.81	0.81	2	-
GCF_000179235.2	s__Vulcanococcus sp000179235	79.5503	394	856	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_019104765.1	s__Vulcanococcus sp019104765	79.3635	392	856	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:25:57,121] [INFO] GTDB search result was written to OceanDNA-b16719/result_gtdb.tsv
[2023-03-15 17:25:57,121] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:25:57,123] [INFO] DFAST_QC result json was written to OceanDNA-b16719/dqc_result.json
[2023-03-15 17:25:57,123] [INFO] DFAST_QC completed!
[2023-03-15 17:25:57,123] [INFO] Total running time: 0h1m56s