[2024-01-24 13:28:12,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:12,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:12,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference
[2024-01-24 13:28:13,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,439] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg9013ef99-d48a-45c8-ada6-003b790bdedc/GCF_020097835.1_ASM2009783v1_genomic.fna.gz | prodigal -d GCF_020097835.1_ASM2009783v1_genomic.fna/cds.fna -a GCF_020097835.1_ASM2009783v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:33,450] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:33,450] [INFO] Task started: HMMsearch
[2024-01-24 13:28:33,450] [INFO] Running command: hmmsearch --tblout GCF_020097835.1_ASM2009783v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference/reference_markers.hmm GCF_020097835.1_ASM2009783v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:33,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:33,825] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9013ef99-d48a-45c8-ada6-003b790bdedc/GCF_020097835.1_ASM2009783v1_genomic.fna.gz]
[2024-01-24 13:28:33,879] [INFO] Query marker FASTA was written to GCF_020097835.1_ASM2009783v1_genomic.fna/markers.fasta
[2024-01-24 13:28:33,879] [INFO] Task started: Blastn
[2024-01-24 13:28:33,879] [INFO] Running command: blastn -query GCF_020097835.1_ASM2009783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference/reference_markers.fasta -out GCF_020097835.1_ASM2009783v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:34,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:34,457] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:34,457] [INFO] Target genome list was writen to GCF_020097835.1_ASM2009783v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:34,469] [INFO] Task started: fastANI
[2024-01-24 13:28:34,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg9013ef99-d48a-45c8-ada6-003b790bdedc/GCF_020097835.1_ASM2009783v1_genomic.fna.gz --refList GCF_020097835.1_ASM2009783v1_genomic.fna/target_genomes.txt --output GCF_020097835.1_ASM2009783v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:46,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:46,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:46,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:46,254] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:46,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:46,255] [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
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	88.6797	963	1313	95	below_threshold
Haloprofundus marisrubri	strain=SB9	GCA_001469955.1	1514971	1514971	type	True	86.271	934	1313	95	below_threshold
Halogranum amylolyticum	strain=CGMCC 1.10121	GCA_900110465.1	660520	660520	type	True	79.8727	649	1313	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	79.6446	573	1313	95	below_threshold
Haloferax sulfurifontis	strain=CCM 7217	GCA_014635105.1	255616	255616	type	True	79.5935	584	1313	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	79.5758	612	1313	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	79.5541	606	1313	95	below_threshold
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	79.5385	635	1313	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	79.4124	587	1313	95	below_threshold
Halogranum rubrum	strain=CGMCC 1.7738	GCA_900114455.1	553466	553466	type	True	79.3537	660	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,256] [INFO] DFAST Taxonomy check result was written to GCF_020097835.1_ASM2009783v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:46,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:46,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:46,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference/checkm_data
[2024-01-24 13:28:46,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:46,300] [INFO] Task started: CheckM
[2024-01-24 13:28:46,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097835.1_ASM2009783v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097835.1_ASM2009783v1_genomic.fna/checkm_input GCF_020097835.1_ASM2009783v1_genomic.fna/checkm_result
[2024-01-24 13:29:40,502] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:40,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:40,523] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:40,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:40,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097835.1_ASM2009783v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:40,525] [INFO] Task started: Blastn
[2024-01-24 13:29:40,525] [INFO] Running command: blastn -query GCF_020097835.1_ASM2009783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg793ee4ef-32be-411c-9e42-781d4463d2fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097835.1_ASM2009783v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:41,107] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:41,111] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:41,112] [INFO] Target genome list was writen to GCF_020097835.1_ASM2009783v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:41,121] [INFO] Task started: fastANI
[2024-01-24 13:29:41,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg9013ef99-d48a-45c8-ada6-003b790bdedc/GCF_020097835.1_ASM2009783v1_genomic.fna.gz --refList GCF_020097835.1_ASM2009783v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097835.1_ASM2009783v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:51,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:51,492] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:51,493] [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_003439925.1	s__Haloprofundus halophilus	88.6654	964	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	98.76	98.76	0.93	0.93	2	-
GCF_001469955.1	s__Haloprofundus marisrubri	86.271	934	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110465.1	s__Halogranum amylolyticum	79.8428	653	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844195.1	s__Halegenticoccus soli	79.6917	644	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025685.1	s__Haloferax volcanii	79.6733	578	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
GCF_000337835.1	s__Haloferax sulfurifontis	79.6663	574	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	99.04	99.04	0.92	0.92	2	-
GCF_900112175.1	s__Halogeometricum rufum	79.6076	608	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_000336775.1	s__Haloferax gibbonsii	79.5871	602	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_000336815.1	s__Haloferax prahovense	79.437	584	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
GCF_900114455.1	s__Halogranum rubrum	79.3646	659	1313	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	97.00	97.00	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:51,494] [INFO] GTDB search result was written to GCF_020097835.1_ASM2009783v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:51,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:51,501] [INFO] DFAST_QC result json was written to GCF_020097835.1_ASM2009783v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:51,501] [INFO] DFAST_QC completed!
[2024-01-24 13:29:51,501] [INFO] Total running time: 0h1m39s