[2024-01-24 15:18:26,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference
[2024-01-24 15:18:28,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,177] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f0af9bd-609c-44cc-af83-3e9c50f0589b/GCF_002844555.1_ASM284455v1_genomic.fna.gz | prodigal -d GCF_002844555.1_ASM284455v1_genomic.fna/cds.fna -a GCF_002844555.1_ASM284455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:41,046] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:41,046] [INFO] Task started: HMMsearch
[2024-01-24 15:18:41,046] [INFO] Running command: hmmsearch --tblout GCF_002844555.1_ASM284455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference/reference_markers.hmm GCF_002844555.1_ASM284455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:41,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:41,336] [INFO] Found 6/6 markers.
[2024-01-24 15:18:41,366] [INFO] Query marker FASTA was written to GCF_002844555.1_ASM284455v1_genomic.fna/markers.fasta
[2024-01-24 15:18:41,366] [INFO] Task started: Blastn
[2024-01-24 15:18:41,366] [INFO] Running command: blastn -query GCF_002844555.1_ASM284455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference/reference_markers.fasta -out GCF_002844555.1_ASM284455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:42,011] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:42,015] [INFO] Selected 23 target genomes.
[2024-01-24 15:18:42,015] [INFO] Target genome list was writen to GCF_002844555.1_ASM284455v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:42,026] [INFO] Task started: fastANI
[2024-01-24 15:18:42,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0af9bd-609c-44cc-af83-3e9c50f0589b/GCF_002844555.1_ASM284455v1_genomic.fna.gz --refList GCF_002844555.1_ASM284455v1_genomic.fna/target_genomes.txt --output GCF_002844555.1_ASM284455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:58,434] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:58,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:58,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:58,446] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:58,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:58,446] [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
Brumimicrobium salinarum	strain=LHR20	GCA_002844555.1	2058658	2058658	type	True	100.0	1107	1109	95	conclusive
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	78.6839	319	1109	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	78.1767	384	1109	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	78.0159	317	1109	95	below_threshold
Lishizhenia tianjinensis	strain=CGMCC 1.7005	GCA_900116425.1	477690	477690	type	True	76.7936	56	1109	95	below_threshold
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.2293	51	1109	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.0644	54	1109	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:58,448] [INFO] DFAST Taxonomy check result was written to GCF_002844555.1_ASM284455v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:58,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:58,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:58,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference/checkm_data
[2024-01-24 15:18:58,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:58,491] [INFO] Task started: CheckM
[2024-01-24 15:18:58,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002844555.1_ASM284455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002844555.1_ASM284455v1_genomic.fna/checkm_input GCF_002844555.1_ASM284455v1_genomic.fna/checkm_result
[2024-01-24 15:19:38,611] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:38,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:38,634] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:38,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:38,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002844555.1_ASM284455v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:38,635] [INFO] Task started: Blastn
[2024-01-24 15:19:38,635] [INFO] Running command: blastn -query GCF_002844555.1_ASM284455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6873f9a7-7253-4835-aee9-6fd3ff5e32d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002844555.1_ASM284455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:39,492] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:39,502] [INFO] Selected 19 target genomes.
[2024-01-24 15:19:39,503] [INFO] Target genome list was writen to GCF_002844555.1_ASM284455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:39,518] [INFO] Task started: fastANI
[2024-01-24 15:19:39,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0af9bd-609c-44cc-af83-3e9c50f0589b/GCF_002844555.1_ASM284455v1_genomic.fna.gz --refList GCF_002844555.1_ASM284455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002844555.1_ASM284455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:51,601] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:51,612] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:51,613] [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_002844555.1	s__Brumimicrobium salinarum	100.0	1107	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003143775.1	s__Brumimicrobium sp003143775	78.9025	371	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402975.1	s__Brumimicrobium aurantiacum	78.6706	320	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	78.1814	384	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025005.1	s__Brumimicrobium mesophilum	78.0046	318	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734085.1	s__Brumimicrobium sp002734085	76.9209	121	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.2293	51	1109	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:51,615] [INFO] GTDB search result was written to GCF_002844555.1_ASM284455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:51,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:51,619] [INFO] DFAST_QC result json was written to GCF_002844555.1_ASM284455v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:51,619] [INFO] DFAST_QC completed!
[2024-01-24 15:19:51,619] [INFO] Total running time: 0h1m25s