[2024-01-24 11:26:28,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,011] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference
[2024-01-24 11:26:29,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,362] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg563d18b4-75b2-4a8e-9aed-cb43fedfe0ef/GCF_003841485.1_ASM384148v1_genomic.fna.gz | prodigal -d GCF_003841485.1_ASM384148v1_genomic.fna/cds.fna -a GCF_003841485.1_ASM384148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:46,055] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:46,056] [INFO] Task started: HMMsearch
[2024-01-24 11:26:46,056] [INFO] Running command: hmmsearch --tblout GCF_003841485.1_ASM384148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference/reference_markers.hmm GCF_003841485.1_ASM384148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:46,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:46,317] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg563d18b4-75b2-4a8e-9aed-cb43fedfe0ef/GCF_003841485.1_ASM384148v1_genomic.fna.gz]
[2024-01-24 11:26:46,346] [INFO] Query marker FASTA was written to GCF_003841485.1_ASM384148v1_genomic.fna/markers.fasta
[2024-01-24 11:26:46,346] [INFO] Task started: Blastn
[2024-01-24 11:26:46,347] [INFO] Running command: blastn -query GCF_003841485.1_ASM384148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference/reference_markers.fasta -out GCF_003841485.1_ASM384148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,947] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,950] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:46,950] [INFO] Target genome list was writen to GCF_003841485.1_ASM384148v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,970] [INFO] Task started: fastANI
[2024-01-24 11:26:46,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg563d18b4-75b2-4a8e-9aed-cb43fedfe0ef/GCF_003841485.1_ASM384148v1_genomic.fna.gz --refList GCF_003841485.1_ASM384148v1_genomic.fna/target_genomes.txt --output GCF_003841485.1_ASM384148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:58,909] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:58,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:58,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:58,922] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:58,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:58,922] [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
Natrarchaeobius halalkaliphilus	strain=AArcht-Sl	GCA_003841485.1	1679091	1679091	type	True	100.0	1165	1165	95	conclusive
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	79.7495	536	1165	95	below_threshold
Natronorubrum aibiense	strain=7-3	GCA_009392895.1	348826	348826	type	True	79.6625	507	1165	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	79.6078	554	1165	95	below_threshold
Natronorubrum tibetense	strain=GA33	GCA_000383975.1	63128	63128	type	True	79.473	549	1165	95	below_threshold
Natronorubrum tibetense	strain=GA33	GCA_000337235.1	63128	63128	type	True	79.443	549	1165	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.4185	497	1165	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	79.367	542	1165	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.3322	496	1165	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	79.322	534	1165	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	79.2816	535	1165	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	79.2195	573	1165	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	79.1763	545	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:58,925] [INFO] DFAST Taxonomy check result was written to GCF_003841485.1_ASM384148v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:58,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:58,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:58,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference/checkm_data
[2024-01-24 11:26:58,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:58,969] [INFO] Task started: CheckM
[2024-01-24 11:26:58,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003841485.1_ASM384148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003841485.1_ASM384148v1_genomic.fna/checkm_input GCF_003841485.1_ASM384148v1_genomic.fna/checkm_result
[2024-01-24 11:27:46,619] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:46,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:46,647] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:46,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:46,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003841485.1_ASM384148v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:46,649] [INFO] Task started: Blastn
[2024-01-24 11:27:46,649] [INFO] Running command: blastn -query GCF_003841485.1_ASM384148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62be227b-320c-4588-823d-5647adcfff57/dqc_reference/reference_markers_gtdb.fasta -out GCF_003841485.1_ASM384148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:47,494] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:47,496] [INFO] Selected 11 target genomes.
[2024-01-24 11:27:47,497] [INFO] Target genome list was writen to GCF_003841485.1_ASM384148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:47,508] [INFO] Task started: fastANI
[2024-01-24 11:27:47,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg563d18b4-75b2-4a8e-9aed-cb43fedfe0ef/GCF_003841485.1_ASM384148v1_genomic.fna.gz --refList GCF_003841485.1_ASM384148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003841485.1_ASM384148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:57,945] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:57,965] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:57,966] [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_003841485.1	s__Natrarchaeobius halalkaliphilus	100.0	1165	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003841465.1	s__Natrarchaeobius chitinivorans_A	82.0681	800	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003841505.1	s__Natrarchaeobius chitinivorans	81.4027	661	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008245225.1	s__Natrarchaeobius swarupiae	80.3813	619	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	96.49	96.49	0.86	0.86	2	-
GCF_000217715.1	s__Halopiger xanaduensis	79.6439	551	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009392895.1	s__Natronorubrum aibiense	79.6072	513	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	79.533	541	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000383975.1	s__Natronorubrum tibetense	79.4572	549	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900110455.1	s__Natrinema salifodinae	79.4099	498	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900112205.1	s__Halobiforma haloterrestris	79.3463	544	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	79.2674	537	1165	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:57,968] [INFO] GTDB search result was written to GCF_003841485.1_ASM384148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:57,968] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:57,974] [INFO] DFAST_QC result json was written to GCF_003841485.1_ASM384148v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:57,975] [INFO] DFAST_QC completed!
[2024-01-24 11:27:57,975] [INFO] Total running time: 0h1m30s