[2024-01-25 19:00:35,835] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:35,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:35,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference
[2024-01-25 19:00:37,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:37,082] [INFO] Task started: Prodigal
[2024-01-25 19:00:37,082] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9a5f87b-b54b-4482-942b-8afb51ae2313/GCF_027257905.1_ASM2725790v1_genomic.fna.gz | prodigal -d GCF_027257905.1_ASM2725790v1_genomic.fna/cds.fna -a GCF_027257905.1_ASM2725790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:59,394] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:59,395] [INFO] Task started: HMMsearch
[2024-01-25 19:00:59,395] [INFO] Running command: hmmsearch --tblout GCF_027257905.1_ASM2725790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference/reference_markers.hmm GCF_027257905.1_ASM2725790v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:59,626] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:59,627] [INFO] Found 6/6 markers.
[2024-01-25 19:00:59,664] [INFO] Query marker FASTA was written to GCF_027257905.1_ASM2725790v1_genomic.fna/markers.fasta
[2024-01-25 19:00:59,665] [INFO] Task started: Blastn
[2024-01-25 19:00:59,665] [INFO] Running command: blastn -query GCF_027257905.1_ASM2725790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference/reference_markers.fasta -out GCF_027257905.1_ASM2725790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:00,293] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:00,296] [INFO] Selected 19 target genomes.
[2024-01-25 19:01:00,296] [INFO] Target genome list was writen to GCF_027257905.1_ASM2725790v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:00,314] [INFO] Task started: fastANI
[2024-01-25 19:01:00,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9a5f87b-b54b-4482-942b-8afb51ae2313/GCF_027257905.1_ASM2725790v1_genomic.fna.gz --refList GCF_027257905.1_ASM2725790v1_genomic.fna/target_genomes.txt --output GCF_027257905.1_ASM2725790v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:16,365] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:16,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:16,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:16,371] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:16,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:16,371] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	77.9383	176	1487	95	below_threshold
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	77.3371	147	1487	95	below_threshold
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.5945	90	1487	95	below_threshold
Pelagicoccus enzymogenes	strain=NFK12	GCA_014803405.1	2773457	2773457	type	True	76.1512	54	1487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:16,373] [INFO] DFAST Taxonomy check result was written to GCF_027257905.1_ASM2725790v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:16,373] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:16,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:16,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference/checkm_data
[2024-01-25 19:01:16,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:16,417] [INFO] Task started: CheckM
[2024-01-25 19:01:16,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027257905.1_ASM2725790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027257905.1_ASM2725790v1_genomic.fna/checkm_input GCF_027257905.1_ASM2725790v1_genomic.fna/checkm_result
[2024-01-25 19:02:17,113] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:17,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:17,131] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:17,131] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:17,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027257905.1_ASM2725790v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:17,133] [INFO] Task started: Blastn
[2024-01-25 19:02:17,133] [INFO] Running command: blastn -query GCF_027257905.1_ASM2725790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg373aba27-5636-4d6b-a0e1-7282bcce18f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_027257905.1_ASM2725790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:18,300] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:18,305] [INFO] Selected 19 target genomes.
[2024-01-25 19:02:18,305] [INFO] Target genome list was writen to GCF_027257905.1_ASM2725790v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:18,331] [INFO] Task started: fastANI
[2024-01-25 19:02:18,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9a5f87b-b54b-4482-942b-8afb51ae2313/GCF_027257905.1_ASM2725790v1_genomic.fna.gz --refList GCF_027257905.1_ASM2725790v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027257905.1_ASM2725790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:33,191] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:33,200] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:02:33,201] [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_003185655.1	s__WN38 sp003185655	77.9748	174	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566795.1	s__WN38 sp003566795	77.6836	118	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025905.1	s__Coraliomargarita akajimensis	77.3371	147	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729725.1	s__UBA7441 sp002729725	77.2024	141	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
GCA_002480015.1	s__UBA7441 sp002480015	77.1639	113	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	-
GCA_007692545.1	s__UBA7441 sp007692545	77.1459	105	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908325.1	s__UBA7441 sp009908325	77.0369	127	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728235.1	s__BACL24 sp902728235	76.853	130	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
GCA_002430605.1	s__BACL24 sp002430605	76.8303	90	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.69	99.69	0.90	0.90	2	-
GCA_017854655.1	s__BACL24 sp017854655	76.6017	77	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
GCA_905479975.1	s__BACL24 sp905479975	76.5625	135	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607135.1	s__BACL24 sp003485085	76.1767	85	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
GCA_002469895.1	s__Coraliomargarita sp002469895	76.1758	56	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	99.42	99.21	0.91	0.88	4	-
GCA_903898675.1	s__Lacunisphaera sp903898675	75.7525	53	1487	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:33,202] [INFO] GTDB search result was written to GCF_027257905.1_ASM2725790v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:33,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:33,205] [INFO] DFAST_QC result json was written to GCF_027257905.1_ASM2725790v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:33,206] [INFO] DFAST_QC completed!
[2024-01-25 19:02:33,206] [INFO] Total running time: 0h1m57s