[2024-01-25 20:14:05,837] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:05,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:05,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference
[2024-01-25 20:14:07,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:07,010] [INFO] Task started: Prodigal
[2024-01-25 20:14:07,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg55744a94-cf2e-4b33-a00b-7e49c0f9c1bc/GCF_003611635.1_ASM361163v1_genomic.fna.gz | prodigal -d GCF_003611635.1_ASM361163v1_genomic.fna/cds.fna -a GCF_003611635.1_ASM361163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:06,869] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:06,869] [INFO] Task started: HMMsearch
[2024-01-25 20:15:06,870] [INFO] Running command: hmmsearch --tblout GCF_003611635.1_ASM361163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference/reference_markers.hmm GCF_003611635.1_ASM361163v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:07,334] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:07,336] [INFO] Found 6/6 markers.
[2024-01-25 20:15:07,423] [INFO] Query marker FASTA was written to GCF_003611635.1_ASM361163v1_genomic.fna/markers.fasta
[2024-01-25 20:15:07,423] [INFO] Task started: Blastn
[2024-01-25 20:15:07,423] [INFO] Running command: blastn -query GCF_003611635.1_ASM361163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference/reference_markers.fasta -out GCF_003611635.1_ASM361163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:08,155] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:08,158] [INFO] Selected 13 target genomes.
[2024-01-25 20:15:08,159] [INFO] Target genome list was writen to GCF_003611635.1_ASM361163v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:08,174] [INFO] Task started: fastANI
[2024-01-25 20:15:08,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg55744a94-cf2e-4b33-a00b-7e49c0f9c1bc/GCF_003611635.1_ASM361163v1_genomic.fna.gz --refList GCF_003611635.1_ASM361163v1_genomic.fna/target_genomes.txt --output GCF_003611635.1_ASM361163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:37,841] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:37,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:37,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:37,851] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:37,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:37,851] [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
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	100.0	3040	3070	95	conclusive
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	93.5363	2418	3070	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	92.1463	2494	3070	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	89.8717	2110	3070	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	89.7703	2235	3070	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	88.5866	2188	3070	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	88.3242	2124	3070	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4876	316	3070	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.4748	325	3070	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.449	319	3070	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.1073	153	3070	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	75.0063	123	3070	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	74.9377	344	3070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:37,853] [INFO] DFAST Taxonomy check result was written to GCF_003611635.1_ASM361163v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:37,854] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:37,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:37,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference/checkm_data
[2024-01-25 20:15:37,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:37,948] [INFO] Task started: CheckM
[2024-01-25 20:15:37,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003611635.1_ASM361163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003611635.1_ASM361163v1_genomic.fna/checkm_input GCF_003611635.1_ASM361163v1_genomic.fna/checkm_result
[2024-01-25 20:20:35,477] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:35,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:35,508] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:35,509] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:35,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003611635.1_ASM361163v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:35,510] [INFO] Task started: Blastn
[2024-01-25 20:20:35,510] [INFO] Running command: blastn -query GCF_003611635.1_ASM361163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14e5b7ca-ec7d-4650-a293-1ccd32bfcb69/dqc_reference/reference_markers_gtdb.fasta -out GCF_003611635.1_ASM361163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:36,906] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:36,912] [INFO] Selected 7 target genomes.
[2024-01-25 20:20:36,912] [INFO] Target genome list was writen to GCF_003611635.1_ASM361163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:36,924] [INFO] Task started: fastANI
[2024-01-25 20:20:36,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg55744a94-cf2e-4b33-a00b-7e49c0f9c1bc/GCF_003611635.1_ASM361163v1_genomic.fna.gz --refList GCF_003611635.1_ASM361163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003611635.1_ASM361163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:59,737] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:59,742] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:59,743] [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_003611635.1	s__Corallococcus terminator	100.0	3040	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003612115.1	s__Corallococcus sp003612115	93.5922	2499	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.04	99.04	0.92	0.92	2	-
GCA_004173515.1	s__Corallococcus sp004173515	92.9475	2314	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014930455.1	s__Corallococcus sp014930455	92.17	2491	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611735.1	s__Corallococcus sicarius	89.8039	2229	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611675.1	s__Corallococcus sp003611675	89.7105	2200	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017302985.1	s__Corallococcus macrosporus_A	88.2335	2335	3070	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:59,744] [INFO] GTDB search result was written to GCF_003611635.1_ASM361163v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:59,746] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:59,748] [INFO] DFAST_QC result json was written to GCF_003611635.1_ASM361163v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:59,748] [INFO] DFAST_QC completed!
[2024-01-25 20:20:59,749] [INFO] Total running time: 0h6m54s