[2024-01-24 12:39:40,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:40,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:40,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference
[2024-01-24 12:39:41,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:41,723] [INFO] Task started: Prodigal
[2024-01-24 12:39:41,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg34622e22-13ed-4999-b786-eabea2a3597b/GCF_004116405.1_ASM411640v1_genomic.fna.gz | prodigal -d GCF_004116405.1_ASM411640v1_genomic.fna/cds.fna -a GCF_004116405.1_ASM411640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:05,929] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:05,930] [INFO] Task started: HMMsearch
[2024-01-24 12:40:05,930] [INFO] Running command: hmmsearch --tblout GCF_004116405.1_ASM411640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference/reference_markers.hmm GCF_004116405.1_ASM411640v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:06,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:06,205] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg34622e22-13ed-4999-b786-eabea2a3597b/GCF_004116405.1_ASM411640v1_genomic.fna.gz]
[2024-01-24 12:40:06,256] [INFO] Query marker FASTA was written to GCF_004116405.1_ASM411640v1_genomic.fna/markers.fasta
[2024-01-24 12:40:06,256] [INFO] Task started: Blastn
[2024-01-24 12:40:06,257] [INFO] Running command: blastn -query GCF_004116405.1_ASM411640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference/reference_markers.fasta -out GCF_004116405.1_ASM411640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:06,885] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:06,889] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:06,890] [INFO] Target genome list was writen to GCF_004116405.1_ASM411640v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:06,904] [INFO] Task started: fastANI
[2024-01-24 12:40:06,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg34622e22-13ed-4999-b786-eabea2a3597b/GCF_004116405.1_ASM411640v1_genomic.fna.gz --refList GCF_004116405.1_ASM411640v1_genomic.fna/target_genomes.txt --output GCF_004116405.1_ASM411640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:17,243] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:17,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:17,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:17,254] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:17,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:17,254] [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
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	100.0	1623	1623	95	conclusive
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	84.5697	1042	1623	95	below_threshold
Halogranum amylolyticum	strain=CGMCC 1.10121	GCA_900110465.1	660520	660520	type	True	79.5283	688	1623	95	below_threshold
Haloferax sulfurifontis	strain=ATCC BAA-897	GCA_000337835.1	255616	255616	type	True	79.3015	557	1623	95	below_threshold
Haloferax denitrificans	strain=ATCC 35960	GCA_000337795.1	35745	35745	type	True	79.2501	563	1623	95	below_threshold
Halogranum gelatinilyticum	strain=CGMCC 1.10119	GCA_900103715.1	660521	660521	type	True	79.2448	603	1623	95	below_threshold
Haloferax sulfurifontis	strain=CCM 7217	GCA_014635105.1	255616	255616	type	True	79.151	563	1623	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000025685.1	2246	2246	type	True	79.085	551	1623	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	79.0658	543	1623	95	below_threshold
Halobaculum halophilum	strain=Gai3-2	GCA_013401515.1	2743090	2743090	type	True	78.451	551	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:17,256] [INFO] DFAST Taxonomy check result was written to GCF_004116405.1_ASM411640v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:17,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:17,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:17,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference/checkm_data
[2024-01-24 12:40:17,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:17,304] [INFO] Task started: CheckM
[2024-01-24 12:40:17,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116405.1_ASM411640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116405.1_ASM411640v1_genomic.fna/checkm_input GCF_004116405.1_ASM411640v1_genomic.fna/checkm_result
[2024-01-24 12:41:20,210] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:20,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:20,245] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:20,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:20,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116405.1_ASM411640v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:20,246] [INFO] Task started: Blastn
[2024-01-24 12:41:20,247] [INFO] Running command: blastn -query GCF_004116405.1_ASM411640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4aea7fd-d522-4c67-b1b1-81f6bf142812/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116405.1_ASM411640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:20,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:20,799] [INFO] Selected 10 target genomes.
[2024-01-24 12:41:20,799] [INFO] Target genome list was writen to GCF_004116405.1_ASM411640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:20,805] [INFO] Task started: fastANI
[2024-01-24 12:41:20,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg34622e22-13ed-4999-b786-eabea2a3597b/GCF_004116405.1_ASM411640v1_genomic.fna.gz --refList GCF_004116405.1_ASM411640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116405.1_ASM411640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:32,543] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:32,554] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:32,555] [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
GCA_004116405.1	s__Halegenticoccus sp004116405	100.0	1623	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002844195.1	s__Halegenticoccus soli	84.5994	1039	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110465.1	s__Halogranum amylolyticum	79.4895	694	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337835.1	s__Haloferax sulfurifontis	79.3326	553	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	99.04	99.04	0.92	0.92	2	-
GCF_000337795.1	s__Haloferax denitrificans	79.2498	564	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	N/A	N/A	N/A	N/A	1	-
GCF_900103715.1	s__Halogranum gelatinilyticum	79.2496	602	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336775.1	s__Haloferax gibbonsii	79.1488	572	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_000025685.1	s__Haloferax volcanii	79.0569	554	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
GCF_900114455.1	s__Halogranum rubrum	78.6842	580	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	97.00	97.00	0.87	0.87	2	-
GCF_013401515.1	s__Halobaculum sp013401515	78.4932	546	1623	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:32,556] [INFO] GTDB search result was written to GCF_004116405.1_ASM411640v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:32,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:32,564] [INFO] DFAST_QC result json was written to GCF_004116405.1_ASM411640v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:32,564] [INFO] DFAST_QC completed!
[2024-01-24 12:41:32,564] [INFO] Total running time: 0h1m52s