[2024-01-24 12:40:50,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference
[2024-01-24 12:40:51,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,931] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg6639558a-06c6-4b02-baa9-f7505f523b9c/GCF_024300625.1_ASM2430062v1_genomic.fna.gz | prodigal -d GCF_024300625.1_ASM2430062v1_genomic.fna/cds.fna -a GCF_024300625.1_ASM2430062v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:08,688] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:08,688] [INFO] Task started: HMMsearch
[2024-01-24 12:41:08,688] [INFO] Running command: hmmsearch --tblout GCF_024300625.1_ASM2430062v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference/reference_markers.hmm GCF_024300625.1_ASM2430062v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:08,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:08,936] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6639558a-06c6-4b02-baa9-f7505f523b9c/GCF_024300625.1_ASM2430062v1_genomic.fna.gz]
[2024-01-24 12:41:08,967] [INFO] Query marker FASTA was written to GCF_024300625.1_ASM2430062v1_genomic.fna/markers.fasta
[2024-01-24 12:41:08,968] [INFO] Task started: Blastn
[2024-01-24 12:41:08,968] [INFO] Running command: blastn -query GCF_024300625.1_ASM2430062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference/reference_markers.fasta -out GCF_024300625.1_ASM2430062v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:09,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:09,491] [INFO] Selected 9 target genomes.
[2024-01-24 12:41:09,491] [INFO] Target genome list was writen to GCF_024300625.1_ASM2430062v1_genomic.fna/target_genomes.txt
[2024-01-24 12:41:09,496] [INFO] Task started: fastANI
[2024-01-24 12:41:09,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg6639558a-06c6-4b02-baa9-f7505f523b9c/GCF_024300625.1_ASM2430062v1_genomic.fna.gz --refList GCF_024300625.1_ASM2430062v1_genomic.fna/target_genomes.txt --output GCF_024300625.1_ASM2430062v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:16,089] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:16,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:16,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:16,104] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:41:16,105] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:41:16,105] [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
Halovivax limisalsi	strain=IBRC-M 10022	GCA_023093535.1	1453760	1453760	type	True	80.0885	629	1233	95	below_threshold
Halovivax ruber	strain=XH-70	GCA_000328525.1	387341	387341	type	True	79.7551	551	1233	95	below_threshold
Halovivax asiaticus	strain=JCM 14624	GCA_000337515.1	332953	332953	type	True	79.69	517	1233	95	below_threshold
Halovivax cerinus	strain=IBRC-M 10256	GCA_024498195.1	1487865	1487865	type	True	79.4422	594	1233	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	77.941	429	1233	95	below_threshold
Haloterrigena daqingensis	strain=JX313	GCA_001971705.1	588898	588898	type	True	77.594	372	1233	95	below_threshold
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	77.5071	410	1233	95	below_threshold
Halococcus salsus	strain=ZJ1	GCA_009900715.1	2162894	2162894	type	True	76.5097	201	1233	95	below_threshold
Halorubrum kocurii	strain=JCM 14978	GCA_000337355.1	478441	478441	type	True	76.4999	247	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:16,108] [INFO] DFAST Taxonomy check result was written to GCF_024300625.1_ASM2430062v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:16,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:16,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:16,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference/checkm_data
[2024-01-24 12:41:16,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:16,150] [INFO] Task started: CheckM
[2024-01-24 12:41:16,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024300625.1_ASM2430062v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024300625.1_ASM2430062v1_genomic.fna/checkm_input GCF_024300625.1_ASM2430062v1_genomic.fna/checkm_result
[2024-01-24 12:42:03,533] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:03,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:03,561] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:03,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:03,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024300625.1_ASM2430062v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:03,562] [INFO] Task started: Blastn
[2024-01-24 12:42:03,562] [INFO] Running command: blastn -query GCF_024300625.1_ASM2430062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1a7b1b-0efb-4c2a-8acd-eeea57c26810/dqc_reference/reference_markers_gtdb.fasta -out GCF_024300625.1_ASM2430062v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:04,074] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:04,078] [INFO] Selected 12 target genomes.
[2024-01-24 12:42:04,078] [INFO] Target genome list was writen to GCF_024300625.1_ASM2430062v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:04,143] [INFO] Task started: fastANI
[2024-01-24 12:42:04,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg6639558a-06c6-4b02-baa9-f7505f523b9c/GCF_024300625.1_ASM2430062v1_genomic.fna.gz --refList GCF_024300625.1_ASM2430062v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024300625.1_ASM2430062v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:12,575] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:12,587] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:42:12,587] [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_000328525.1	s__Halovivax ruber	79.7551	551	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337515.1	s__Halovivax asiaticus	79.7034	515	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119345.1	s__Halovivax sp007119345	79.4543	552	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017357105.1	s__Tc-Br11 sp017357105	78.1369	397	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	78.0226	414	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344565.1	s__Saliphagus sp003344565	77.7764	352	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Saliphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111485.1	s__Natrinema hispanicum_A	77.752	329	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	99.65	99.65	0.93	0.93	2	-
GCF_001971705.1	s__Natronorubrum daqingense	77.6181	369	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003670115.1	s__Natronorubrum sp003670115	77.5145	409	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.42	97.42	0.91	0.91	2	-
GCF_009900715.1	s__Halococcus salsus	76.5388	198	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus	95.0	95.85	95.85	0.78	0.78	2	-
GCF_000337355.1	s__Halorubrum kocurii	76.5198	244	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021085.1	s__PXRE01 sp003021085	76.4628	217	1233	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__PXRE01;g__PXRE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:12,589] [INFO] GTDB search result was written to GCF_024300625.1_ASM2430062v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:12,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:12,593] [INFO] DFAST_QC result json was written to GCF_024300625.1_ASM2430062v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:12,593] [INFO] DFAST_QC completed!
[2024-01-24 12:42:12,593] [INFO] Total running time: 0h1m22s