[2023-06-19 01:24:28,736] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:24:28,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:24:28,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference
[2023-06-19 01:24:30,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:24:30,453] [INFO] Task started: Prodigal
[2023-06-19 01:24:30,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg87ae7719-b5f7-404a-84e6-028117f5ee0b/GCA_018401845.1_ASM1840184v1_genomic.fna.gz | prodigal -d GCA_018401845.1_ASM1840184v1_genomic.fna/cds.fna -a GCA_018401845.1_ASM1840184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:24:47,573] [INFO] Task succeeded: Prodigal
[2023-06-19 01:24:47,574] [INFO] Task started: HMMsearch
[2023-06-19 01:24:47,574] [INFO] Running command: hmmsearch --tblout GCA_018401845.1_ASM1840184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference/reference_markers.hmm GCA_018401845.1_ASM1840184v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:24:47,800] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:24:47,801] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87ae7719-b5f7-404a-84e6-028117f5ee0b/GCA_018401845.1_ASM1840184v1_genomic.fna.gz]
[2023-06-19 01:24:47,834] [INFO] Query marker FASTA was written to GCA_018401845.1_ASM1840184v1_genomic.fna/markers.fasta
[2023-06-19 01:24:47,834] [INFO] Task started: Blastn
[2023-06-19 01:24:47,834] [INFO] Running command: blastn -query GCA_018401845.1_ASM1840184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference/reference_markers.fasta -out GCA_018401845.1_ASM1840184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:24:48,473] [INFO] Task succeeded: Blastn
[2023-06-19 01:24:48,481] [INFO] Selected 28 target genomes.
[2023-06-19 01:24:48,482] [INFO] Target genome list was writen to GCA_018401845.1_ASM1840184v1_genomic.fna/target_genomes.txt
[2023-06-19 01:24:48,491] [INFO] Task started: fastANI
[2023-06-19 01:24:48,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ae7719-b5f7-404a-84e6-028117f5ee0b/GCA_018401845.1_ASM1840184v1_genomic.fna.gz --refList GCA_018401845.1_ASM1840184v1_genomic.fna/target_genomes.txt --output GCA_018401845.1_ASM1840184v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:25:07,103] [INFO] Task succeeded: fastANI
[2023-06-19 01:25:07,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:25:07,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:25:07,114] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:25:07,114] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:25:07,114] [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	78.6945	248	814	95	below_threshold
Gloeobacter morelensis		GCA_021018745.1	2907343	2907343	type	True	75.9547	65	814	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	75.1602	62	814	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.9641	74	814	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.9245	99	814	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.9054	55	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:25:07,117] [INFO] DFAST Taxonomy check result was written to GCA_018401845.1_ASM1840184v1_genomic.fna/tc_result.tsv
[2023-06-19 01:25:07,118] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:25:07,118] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:25:07,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference/checkm_data
[2023-06-19 01:25:07,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:25:07,151] [INFO] Task started: CheckM
[2023-06-19 01:25:07,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018401845.1_ASM1840184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018401845.1_ASM1840184v1_genomic.fna/checkm_input GCA_018401845.1_ASM1840184v1_genomic.fna/checkm_result
[2023-06-19 01:25:57,061] [INFO] Task succeeded: CheckM
[2023-06-19 01:25:57,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.86%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 01:25:57,082] [INFO] ===== Completeness check finished =====
[2023-06-19 01:25:57,082] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:25:57,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018401845.1_ASM1840184v1_genomic.fna/markers.fasta)
[2023-06-19 01:25:57,083] [INFO] Task started: Blastn
[2023-06-19 01:25:57,083] [INFO] Running command: blastn -query GCA_018401845.1_ASM1840184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fc83739-3701-4a6c-bf04-3d4d426bac53/dqc_reference/reference_markers_gtdb.fasta -out GCA_018401845.1_ASM1840184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:25:58,101] [INFO] Task succeeded: Blastn
[2023-06-19 01:25:58,106] [INFO] Selected 20 target genomes.
[2023-06-19 01:25:58,107] [INFO] Target genome list was writen to GCA_018401845.1_ASM1840184v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:25:58,133] [INFO] Task started: fastANI
[2023-06-19 01:25:58,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ae7719-b5f7-404a-84e6-028117f5ee0b/GCA_018401845.1_ASM1840184v1_genomic.fna.gz --refList GCA_018401845.1_ASM1840184v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018401845.1_ASM1840184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:26:08,785] [INFO] Task succeeded: fastANI
[2023-06-19 01:26:08,808] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:26:08,809] [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_018400215.1	s__NIES-981 sp018400215	98.6157	362	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.01	99.01	0.86	0.86	2	conclusive
GCA_018399015.1	s__NIES-981 sp018399015	85.4597	616	814	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_016882525.1	s__NIES-981 sp016882525	83.4143	539	814	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_016882385.1	s__Cyanobium_A sp016882385	82.7838	363	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252665.1	s__Cyanobium_A sp002252665	82.674	524	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697415.1	s__Cyanobium_A sp014697415	82.2056	507	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039265.1	s__NIES-981 sp001039265	82.2004	408	814	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_900088535.1	s__NIES-981 sp900088535	82.1462	533	814	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_016882415.1	s__Vulcanococcus sp016882415	82.0894	266	814	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_000155635.1	s__NIES-981 sp000155635	81.8865	541	814	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_015840335.1	s__Cyanobium_A sp015840335	81.525	502	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029175.1	s__Vulcanococcus sp010029175	81.4246	353	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205255.1	s__Cyanobium_A sp013205255	81.2487	277	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010030955.1	s__Vulcanococcus sp010030955	81.1969	327	814	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_014698445.1	s__Cyanobium elabens	80.9327	497	814	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	80.9035	497	814	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_016882585.1	s__Vulcanococcus sp016882585	80.55	281	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917565.1	s__Cyanobium sp903917565	80.3455	453	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	100.00	99.99	0.99	0.98	6	-
GCA_002737305.1	s__BAIKAL-G1 sp002737305	79.954	302	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463595.1	s__BAIKAL-G1 sp016463595	79.9066	341	814	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:26:08,811] [INFO] GTDB search result was written to GCA_018401845.1_ASM1840184v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:26:08,812] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:26:08,818] [INFO] DFAST_QC result json was written to GCA_018401845.1_ASM1840184v1_genomic.fna/dqc_result.json
[2023-06-19 01:26:08,818] [INFO] DFAST_QC completed!
[2023-06-19 01:26:08,818] [INFO] Total running time: 0h1m40s