[2024-01-24 11:05:25,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference
[2024-01-24 11:05:26,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,883] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgef1681f3-95cf-4cb5-b93f-e6868fdb5bf4/GCF_021249405.1_ASM2124940v1_genomic.fna.gz | prodigal -d GCF_021249405.1_ASM2124940v1_genomic.fna/cds.fna -a GCF_021249405.1_ASM2124940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:41,934] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:41,934] [INFO] Task started: HMMsearch
[2024-01-24 11:05:41,934] [INFO] Running command: hmmsearch --tblout GCF_021249405.1_ASM2124940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference/reference_markers.hmm GCF_021249405.1_ASM2124940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:42,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:42,171] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgef1681f3-95cf-4cb5-b93f-e6868fdb5bf4/GCF_021249405.1_ASM2124940v1_genomic.fna.gz]
[2024-01-24 11:05:42,196] [INFO] Query marker FASTA was written to GCF_021249405.1_ASM2124940v1_genomic.fna/markers.fasta
[2024-01-24 11:05:42,197] [INFO] Task started: Blastn
[2024-01-24 11:05:42,197] [INFO] Running command: blastn -query GCF_021249405.1_ASM2124940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference/reference_markers.fasta -out GCF_021249405.1_ASM2124940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:42,738] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:42,741] [INFO] Selected 8 target genomes.
[2024-01-24 11:05:42,741] [INFO] Target genome list was writen to GCF_021249405.1_ASM2124940v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:42,745] [INFO] Task started: fastANI
[2024-01-24 11:05:42,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgef1681f3-95cf-4cb5-b93f-e6868fdb5bf4/GCF_021249405.1_ASM2124940v1_genomic.fna.gz --refList GCF_021249405.1_ASM2124940v1_genomic.fna/target_genomes.txt --output GCF_021249405.1_ASM2124940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:48,035] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:48,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:48,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:48,044] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:48,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:48,044] [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
Halobacterium litoreum	strain=ZS-54-S2	GCA_021233415.1	2039234	2039234	type	True	82.7648	620	941	95	below_threshold
Halobacterium noricense	strain=JCM 15102	GCA_021233435.1	223182	223182	type	True	82.037	551	941	95	below_threshold
Halobacterium hubeiense	strain=JI20-1	GCA_001488575.1	1407499	1407499	type	True	82.0203	559	941	95	below_threshold
Halobacterium bonnevillei	strain=PCN9	GCA_009831555.1	2692200	2692200	type	True	81.6042	501	941	95	below_threshold
Halobacterium jilantaiense	strain=CGMCC 1.5337	GCA_900110535.1	355548	355548	type	True	81.3757	572	941	95	below_threshold
Halobacterium salinarum	strain=DSM 3754	GCA_008124605.1	2242	2242	type	True	79.8785	406	941	95	below_threshold
Halobacterium salinarum	strain=91-R6	GCA_004799605.1	2242	2242	type	True	79.8377	406	941	95	below_threshold
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	77.9313	329	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:48,046] [INFO] DFAST Taxonomy check result was written to GCF_021249405.1_ASM2124940v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:48,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:48,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:48,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference/checkm_data
[2024-01-24 11:05:48,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:48,083] [INFO] Task started: CheckM
[2024-01-24 11:05:48,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021249405.1_ASM2124940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021249405.1_ASM2124940v1_genomic.fna/checkm_input GCF_021249405.1_ASM2124940v1_genomic.fna/checkm_result
[2024-01-24 11:06:30,737] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:30,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:30,809] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:30,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:30,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021249405.1_ASM2124940v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:30,811] [INFO] Task started: Blastn
[2024-01-24 11:06:30,811] [INFO] Running command: blastn -query GCF_021249405.1_ASM2124940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64940a27-4401-40a8-a178-2c4a5b094335/dqc_reference/reference_markers_gtdb.fasta -out GCF_021249405.1_ASM2124940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:31,323] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:31,327] [INFO] Selected 11 target genomes.
[2024-01-24 11:06:31,327] [INFO] Target genome list was writen to GCF_021249405.1_ASM2124940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:31,336] [INFO] Task started: fastANI
[2024-01-24 11:06:31,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgef1681f3-95cf-4cb5-b93f-e6868fdb5bf4/GCF_021249405.1_ASM2124940v1_genomic.fna.gz --refList GCF_021249405.1_ASM2124940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021249405.1_ASM2124940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:38,913] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:38,926] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:38,926] [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_000230955.2	s__Halobacterium sp000230955	82.4077	598	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741975.1	s__Halobacterium sp009741975	82.3717	497	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011734195.1	s__Halobacterium sp011734195	82.2789	577	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001488575.1	s__Halobacterium hubeiense	82.0122	561	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	99.52	99.49	0.94	0.94	8	-
GCF_001485535.1	s__Halobacterium sp001485535	81.8925	538	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831555.1	s__Halobacterium sp009831555	81.5628	504	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110535.1	s__Halobacterium jilantaiense	81.3516	574	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124605.1	s__Halobacterium salinarum	79.8857	405	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	99.06	98.77	0.91	0.88	7	-
GCF_007833275.1	s__Salarchaeum sp007833275	79.286	403	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Salarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129775.1	s__Halobaculum gomorrense	77.3193	311	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831545.1	s__Halorussus sp008831545	77.2885	319	941	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:38,927] [INFO] GTDB search result was written to GCF_021249405.1_ASM2124940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:38,928] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:38,931] [INFO] DFAST_QC result json was written to GCF_021249405.1_ASM2124940v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:38,931] [INFO] DFAST_QC completed!
[2024-01-24 11:06:38,931] [INFO] Total running time: 0h1m14s