[2024-01-24 14:46:52,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:52,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:52,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference
[2024-01-24 14:46:55,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:55,365] [INFO] Task started: Prodigal
[2024-01-24 14:46:55,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgc15baac9-707f-48c7-868c-404483f9ec6e/GCF_009831455.1_ASM983145v1_genomic.fna.gz | prodigal -d GCF_009831455.1_ASM983145v1_genomic.fna/cds.fna -a GCF_009831455.1_ASM983145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:12,431] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:12,432] [INFO] Task started: HMMsearch
[2024-01-24 14:47:12,432] [INFO] Running command: hmmsearch --tblout GCF_009831455.1_ASM983145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference/reference_markers.hmm GCF_009831455.1_ASM983145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:12,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:12,765] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc15baac9-707f-48c7-868c-404483f9ec6e/GCF_009831455.1_ASM983145v1_genomic.fna.gz]
[2024-01-24 14:47:12,806] [INFO] Query marker FASTA was written to GCF_009831455.1_ASM983145v1_genomic.fna/markers.fasta
[2024-01-24 14:47:12,806] [INFO] Task started: Blastn
[2024-01-24 14:47:12,806] [INFO] Running command: blastn -query GCF_009831455.1_ASM983145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference/reference_markers.fasta -out GCF_009831455.1_ASM983145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:13,378] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:13,381] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:13,382] [INFO] Target genome list was writen to GCF_009831455.1_ASM983145v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:13,389] [INFO] Task started: fastANI
[2024-01-24 14:47:13,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgc15baac9-707f-48c7-868c-404483f9ec6e/GCF_009831455.1_ASM983145v1_genomic.fna.gz --refList GCF_009831455.1_ASM983145v1_genomic.fna/target_genomes.txt --output GCF_009831455.1_ASM983145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:23,831] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:23,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:23,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:23,844] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:23,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:23,844] [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
Salinirussus salinus	strain=YGH44	GCA_009831455.1	1198300	1198300	type	True	100.0	1121	1121	95	conclusive
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	78.6543	494	1121	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.6496	526	1121	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	78.548	423	1121	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	78.4591	448	1121	95	below_threshold
Halosimplex carlsbadense	strain=2-9-1	GCA_000337455.1	171164	171164	type	True	78.404	481	1121	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	78.333	453	1121	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	78.0913	403	1121	95	below_threshold
Halosimplex salinum	strain=YPL4	GCA_003730195.1	1710538	1710538	type	True	77.928	481	1121	95	below_threshold
Haloarcula vallismortis	strain=DSM 3756	GCA_900106715.1	28442	28442	type	True	77.8223	328	1121	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	77.6444	404	1121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:23,846] [INFO] DFAST Taxonomy check result was written to GCF_009831455.1_ASM983145v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:23,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:23,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:23,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference/checkm_data
[2024-01-24 14:47:23,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:23,895] [INFO] Task started: CheckM
[2024-01-24 14:47:23,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009831455.1_ASM983145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009831455.1_ASM983145v1_genomic.fna/checkm_input GCF_009831455.1_ASM983145v1_genomic.fna/checkm_result
[2024-01-24 14:48:11,488] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:11,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:11,513] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:11,514] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:11,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009831455.1_ASM983145v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:11,514] [INFO] Task started: Blastn
[2024-01-24 14:48:11,515] [INFO] Running command: blastn -query GCF_009831455.1_ASM983145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61dd2115-1793-429d-bfb9-acffe2a12156/dqc_reference/reference_markers_gtdb.fasta -out GCF_009831455.1_ASM983145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:12,125] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:12,130] [INFO] Selected 13 target genomes.
[2024-01-24 14:48:12,131] [INFO] Target genome list was writen to GCF_009831455.1_ASM983145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:12,142] [INFO] Task started: fastANI
[2024-01-24 14:48:12,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgc15baac9-707f-48c7-868c-404483f9ec6e/GCF_009831455.1_ASM983145v1_genomic.fna.gz --refList GCF_009831455.1_ASM983145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009831455.1_ASM983145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:22,171] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:22,186] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:22,187] [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_009831455.1	s__Salinirussus salinus	100.0	1121	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Salinirussus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018609945.1	s__SW-9-67-25 sp018609945	78.996	384	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__SW-9-67-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009789175.1	s__Salinibaculum litoreum	78.7677	395	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Salinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415885.1	s__Halosimplex rubrum	78.6577	491	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119205.1	s__Halomicroarcula limicola	78.4992	427	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119195.1	s__Haloarcula salina	78.4327	451	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003022725.1	s__Halovenus sp003022725	78.42	346	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021305.1	s__QH-10-67-22 sp003021305	78.399	358	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QH-10-67-22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831575.1	s__Halovenus sp009831575	78.3359	365	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337455.1	s__Halosimplex carlsbadense	78.3326	490	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675855.1	s__Halostella salina	78.0632	407	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730195.1	s__Halosimplex salinum	77.945	478	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	77.9178	434	1121	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:22,189] [INFO] GTDB search result was written to GCF_009831455.1_ASM983145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:22,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:22,193] [INFO] DFAST_QC result json was written to GCF_009831455.1_ASM983145v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:22,193] [INFO] DFAST_QC completed!
[2024-01-24 14:48:22,194] [INFO] Total running time: 0h1m30s