[2024-01-24 13:40:28,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,145] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1aa3f20-9b28-48e9-831c-ea2c4ea1cf78/GCF_001542905.1_ASM154290v1_genomic.fna.gz | prodigal -d GCF_001542905.1_ASM154290v1_genomic.fna/cds.fna -a GCF_001542905.1_ASM154290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:46,423] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:46,423] [INFO] Task started: HMMsearch
[2024-01-24 13:40:46,423] [INFO] Running command: hmmsearch --tblout GCF_001542905.1_ASM154290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference/reference_markers.hmm GCF_001542905.1_ASM154290v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,680] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb1aa3f20-9b28-48e9-831c-ea2c4ea1cf78/GCF_001542905.1_ASM154290v1_genomic.fna.gz]
[2024-01-24 13:40:46,719] [INFO] Query marker FASTA was written to GCF_001542905.1_ASM154290v1_genomic.fna/markers.fasta
[2024-01-24 13:40:46,719] [INFO] Task started: Blastn
[2024-01-24 13:40:46,719] [INFO] Running command: blastn -query GCF_001542905.1_ASM154290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference/reference_markers.fasta -out GCF_001542905.1_ASM154290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:47,307] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:47,314] [INFO] Selected 5 target genomes.
[2024-01-24 13:40:47,314] [INFO] Target genome list was writen to GCF_001542905.1_ASM154290v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:47,318] [INFO] Task started: fastANI
[2024-01-24 13:40:47,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1aa3f20-9b28-48e9-831c-ea2c4ea1cf78/GCF_001542905.1_ASM154290v1_genomic.fna.gz --refList GCF_001542905.1_ASM154290v1_genomic.fna/target_genomes.txt --output GCF_001542905.1_ASM154290v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:53,194] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:53,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:53,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:53,203] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:53,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:53,204] [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
Halorubrum aethiopicum	strain=SAH-A6	GCA_001542905.1	1758255	1758255	type	True	100.0	1107	1108	95	conclusive
Halorubrum halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	93.3756	765	1108	95	below_threshold
Halorubrum rubrum	strain=YC87	GCA_024494685.1	1126240	1126240	type	True	92.1495	845	1108	95	below_threshold
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	91.2772	834	1108	95	below_threshold
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	90.5209	811	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:53,205] [INFO] DFAST Taxonomy check result was written to GCF_001542905.1_ASM154290v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:53,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:53,206] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:53,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference/checkm_data
[2024-01-24 13:40:53,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:53,243] [INFO] Task started: CheckM
[2024-01-24 13:40:53,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001542905.1_ASM154290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001542905.1_ASM154290v1_genomic.fna/checkm_input GCF_001542905.1_ASM154290v1_genomic.fna/checkm_result
[2024-01-24 13:41:37,578] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:37,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:37,603] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:37,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:37,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001542905.1_ASM154290v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:37,605] [INFO] Task started: Blastn
[2024-01-24 13:41:37,605] [INFO] Running command: blastn -query GCF_001542905.1_ASM154290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf75b31a-0b40-4c73-a056-76beedd701bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001542905.1_ASM154290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:38,351] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:38,355] [INFO] Selected 6 target genomes.
[2024-01-24 13:41:38,356] [INFO] Target genome list was writen to GCF_001542905.1_ASM154290v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:38,367] [INFO] Task started: fastANI
[2024-01-24 13:41:38,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1aa3f20-9b28-48e9-831c-ea2c4ea1cf78/GCF_001542905.1_ASM154290v1_genomic.fna.gz --refList GCF_001542905.1_ASM154290v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001542905.1_ASM154290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:45,479] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,489] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:45,489] [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_001542905.1	s__Halorubrum aethiopicum	100.0	1107	1108	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002252985.1	s__Halorubrum halodurans	93.3542	766	1108	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182635.1	s__Halorubrum cibi	91.2772	834	1108	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113615.1	s__Halorubrum aquaticum	90.5406	810	1108	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697845.1	s__Halorubrum sp003697845	89.4641	823	1108	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287355.1	s__Halorubrum sp003287355	88.5109	780	1108	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,491] [INFO] GTDB search result was written to GCF_001542905.1_ASM154290v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:45,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:45,494] [INFO] DFAST_QC result json was written to GCF_001542905.1_ASM154290v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:45,495] [INFO] DFAST_QC completed!
[2024-01-24 13:41:45,495] [INFO] Total running time: 0h1m17s