[2024-01-24 14:23:14,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:14,270] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:14,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference
[2024-01-24 14:23:15,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:15,467] [INFO] Task started: Prodigal
[2024-01-24 14:23:15,467] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1990fc3-9824-4853-b5d8-136841b62469/GCF_005310945.1_ASM531094v1_genomic.fna.gz | prodigal -d GCF_005310945.1_ASM531094v1_genomic.fna/cds.fna -a GCF_005310945.1_ASM531094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:38,501] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:38,502] [INFO] Task started: HMMsearch
[2024-01-24 14:23:38,502] [INFO] Running command: hmmsearch --tblout GCF_005310945.1_ASM531094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference/reference_markers.hmm GCF_005310945.1_ASM531094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:38,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:38,853] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd1990fc3-9824-4853-b5d8-136841b62469/GCF_005310945.1_ASM531094v1_genomic.fna.gz]
[2024-01-24 14:23:38,899] [INFO] Query marker FASTA was written to GCF_005310945.1_ASM531094v1_genomic.fna/markers.fasta
[2024-01-24 14:23:38,900] [INFO] Task started: Blastn
[2024-01-24 14:23:38,900] [INFO] Running command: blastn -query GCF_005310945.1_ASM531094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference/reference_markers.fasta -out GCF_005310945.1_ASM531094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:39,497] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:39,501] [INFO] Selected 6 target genomes.
[2024-01-24 14:23:39,501] [INFO] Target genome list was writen to GCF_005310945.1_ASM531094v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:39,504] [INFO] Task started: fastANI
[2024-01-24 14:23:39,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1990fc3-9824-4853-b5d8-136841b62469/GCF_005310945.1_ASM531094v1_genomic.fna.gz --refList GCF_005310945.1_ASM531094v1_genomic.fna/target_genomes.txt --output GCF_005310945.1_ASM531094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:46,536] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:46,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:46,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:46,544] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:23:46,544] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:23:46,544] [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
Haloarcula marismortui	strain=ATCC 43049	GCA_005310945.1	2238	2238	suspected-type	True	100.0	1390	1392	95	inconclusive
Haloarcula marismortui	strain=ATCC 43049	GCA_000011085.1	2238	2238	suspected-type	True	99.9973	1387	1392	95	inconclusive
Haloarcula sinaiiensis	strain=ATCC 33800	GCA_018200015.1	35742	35742	suspected-type	True	98.185	1237	1392	95	inconclusive
Haloarcula sinaiiensis	strain=ATCC 33800	GCA_000337275.1	35742	35742	suspected-type	True	98.1663	1213	1392	95	inconclusive
Haloarcula hispanica	strain=CGMCC 1.2049	GCA_000223905.1	51589	51589	type	True	90.8939	1099	1392	95	below_threshold
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	90.7317	988	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:46,546] [INFO] DFAST Taxonomy check result was written to GCF_005310945.1_ASM531094v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:46,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:46,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:46,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference/checkm_data
[2024-01-24 14:23:46,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:46,595] [INFO] Task started: CheckM
[2024-01-24 14:23:46,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005310945.1_ASM531094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005310945.1_ASM531094v1_genomic.fna/checkm_input GCF_005310945.1_ASM531094v1_genomic.fna/checkm_result
[2024-01-24 14:24:50,153] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:50,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:50,175] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:50,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:50,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005310945.1_ASM531094v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:50,176] [INFO] Task started: Blastn
[2024-01-24 14:24:50,176] [INFO] Running command: blastn -query GCF_005310945.1_ASM531094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81d06d05-4913-4284-8a5d-7d50e00eb939/dqc_reference/reference_markers_gtdb.fasta -out GCF_005310945.1_ASM531094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:50,673] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:50,677] [INFO] Selected 7 target genomes.
[2024-01-24 14:24:50,677] [INFO] Target genome list was writen to GCF_005310945.1_ASM531094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:50,683] [INFO] Task started: fastANI
[2024-01-24 14:24:50,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1990fc3-9824-4853-b5d8-136841b62469/GCF_005310945.1_ASM531094v1_genomic.fna.gz --refList GCF_005310945.1_ASM531094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005310945.1_ASM531094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:58,232] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:58,243] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:58,243] [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_000011085.1	s__Haloarcula marismortui	99.9973	1387	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	98.41	98.12	0.88	0.85	9	conclusive
GCF_001485575.1	s__Haloarcula sp001485575	92.2884	1115	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223905.1	s__Haloarcula hispanica	90.8939	1099	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	98.55	97.98	0.94	0.91	11	-
GCA_000336895.1	s__Haloarcula argentinensis	90.5399	1082	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	-
GCF_014647415.1	s__Haloarcula sebkhae	90.1419	1119	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	95.97	95.97	0.88	0.88	2	-
GCF_000336635.1	s__Haloarcula japonica	89.9273	1084	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008729015.1	s__Haloarcula sp008729015	88.3509	1077	1392	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:58,245] [INFO] GTDB search result was written to GCF_005310945.1_ASM531094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:58,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:58,248] [INFO] DFAST_QC result json was written to GCF_005310945.1_ASM531094v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:58,248] [INFO] DFAST_QC completed!
[2024-01-24 14:24:58,249] [INFO] Total running time: 0h1m44s