[2024-01-24 13:31:30,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:30,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:30,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference
[2024-01-24 13:31:32,047] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:32,050] [INFO] Task started: Prodigal
[2024-01-24 13:31:32,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cb97a50-0c14-4b8c-9e65-296edac479b1/GCF_026616205.1_ASM2661620v1_genomic.fna.gz | prodigal -d GCF_026616205.1_ASM2661620v1_genomic.fna/cds.fna -a GCF_026616205.1_ASM2661620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:46,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:46,940] [INFO] Task started: HMMsearch
[2024-01-24 13:31:46,940] [INFO] Running command: hmmsearch --tblout GCF_026616205.1_ASM2661620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference/reference_markers.hmm GCF_026616205.1_ASM2661620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:47,201] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:47,202] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6cb97a50-0c14-4b8c-9e65-296edac479b1/GCF_026616205.1_ASM2661620v1_genomic.fna.gz]
[2024-01-24 13:31:47,231] [INFO] Query marker FASTA was written to GCF_026616205.1_ASM2661620v1_genomic.fna/markers.fasta
[2024-01-24 13:31:47,231] [INFO] Task started: Blastn
[2024-01-24 13:31:47,231] [INFO] Running command: blastn -query GCF_026616205.1_ASM2661620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference/reference_markers.fasta -out GCF_026616205.1_ASM2661620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,791] [INFO] Selected 7 target genomes.
[2024-01-24 13:31:47,791] [INFO] Target genome list was writen to GCF_026616205.1_ASM2661620v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,795] [INFO] Task started: fastANI
[2024-01-24 13:31:47,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb97a50-0c14-4b8c-9e65-296edac479b1/GCF_026616205.1_ASM2661620v1_genomic.fna.gz --refList GCF_026616205.1_ASM2661620v1_genomic.fna/target_genomes.txt --output GCF_026616205.1_ASM2661620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:53,663] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:53,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:53,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:53,673] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:31:53,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:31:53,673] [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
Halolamina salifodinae	strain=DSM 26232	GCA_017874235.1	1202767	1202767	type	True	85.7215	689	1006	95	below_threshold
Halolamina pelagica	strain=CGMCC 1.10329	GCA_900115675.1	699431	699431	type	True	85.3985	665	1006	95	below_threshold
Halolamina rubra	strain=CBA1107	GCA_000739555.1	1380430	1380430	type	True	85.1691	701	1006	95	below_threshold
Halolamina sediminis	strain=halo7	GCA_001282785.1	1480675	1480675	type	True	84.7587	685	1006	95	below_threshold
Halobaculum halophilum	strain=Gai3-2	GCA_013401515.1	2743090	2743090	type	True	78.4333	432	1006	95	below_threshold
Halorubrum tebenquichense	strain=DSM 14210	GCA_000337415.1	119434	119434	type	True	78.0636	383	1006	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	77.5347	385	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:53,675] [INFO] DFAST Taxonomy check result was written to GCF_026616205.1_ASM2661620v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:53,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:53,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:53,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference/checkm_data
[2024-01-24 13:31:53,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:53,713] [INFO] Task started: CheckM
[2024-01-24 13:31:53,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026616205.1_ASM2661620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026616205.1_ASM2661620v1_genomic.fna/checkm_input GCF_026616205.1_ASM2661620v1_genomic.fna/checkm_result
[2024-01-24 13:32:37,380] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:37,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:37,402] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:37,402] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:37,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026616205.1_ASM2661620v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:37,403] [INFO] Task started: Blastn
[2024-01-24 13:32:37,403] [INFO] Running command: blastn -query GCF_026616205.1_ASM2661620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c513ce8-935b-4830-b9cb-e99adf14d69c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026616205.1_ASM2661620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:37,960] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:37,963] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:37,964] [INFO] Target genome list was writen to GCF_026616205.1_ASM2661620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:37,969] [INFO] Task started: fastANI
[2024-01-24 13:32:37,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb97a50-0c14-4b8c-9e65-296edac479b1/GCF_026616205.1_ASM2661620v1_genomic.fna.gz --refList GCF_026616205.1_ASM2661620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026616205.1_ASM2661620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:44,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:44,047] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:32:44,047] [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_017874235.1	s__Halolamina salifodinae	85.7215	689	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115675.1	s__Halolamina pelagica	85.4148	664	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000739555.1	s__Halolamina rubra	85.1532	702	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307315.1	s__Halolamina pelagica_B	85.1023	725	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282785.1	s__Halolamina sediminis	84.7704	684	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025255.2	s__Halolamina sp002025255	84.6107	715	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000224475.1	s__Halolamina sp000224475	80.5689	545	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:44,049] [INFO] GTDB search result was written to GCF_026616205.1_ASM2661620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:44,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:44,054] [INFO] DFAST_QC result json was written to GCF_026616205.1_ASM2661620v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:44,055] [INFO] DFAST_QC completed!
[2024-01-24 13:32:44,055] [INFO] Total running time: 0h1m13s