[2024-01-24 13:18:45,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:45,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:45,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference
[2024-01-24 13:18:47,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,009] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgecbf9348-0fc8-4017-83b9-7d9cdb4888ee/GCF_003730195.1_ASM373019v1_genomic.fna.gz | prodigal -d GCF_003730195.1_ASM373019v1_genomic.fna/cds.fna -a GCF_003730195.1_ASM373019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:11,430] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:11,431] [INFO] Task started: HMMsearch
[2024-01-24 13:19:11,431] [INFO] Running command: hmmsearch --tblout GCF_003730195.1_ASM373019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference/reference_markers.hmm GCF_003730195.1_ASM373019v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:11,655] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:11,656] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgecbf9348-0fc8-4017-83b9-7d9cdb4888ee/GCF_003730195.1_ASM373019v1_genomic.fna.gz]
[2024-01-24 13:19:11,698] [INFO] Query marker FASTA was written to GCF_003730195.1_ASM373019v1_genomic.fna/markers.fasta
[2024-01-24 13:19:11,699] [INFO] Task started: Blastn
[2024-01-24 13:19:11,699] [INFO] Running command: blastn -query GCF_003730195.1_ASM373019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference/reference_markers.fasta -out GCF_003730195.1_ASM373019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:12,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:12,253] [INFO] Selected 6 target genomes.
[2024-01-24 13:19:12,253] [INFO] Target genome list was writen to GCF_003730195.1_ASM373019v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:12,268] [INFO] Task started: fastANI
[2024-01-24 13:19:12,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgecbf9348-0fc8-4017-83b9-7d9cdb4888ee/GCF_003730195.1_ASM373019v1_genomic.fna.gz --refList GCF_003730195.1_ASM373019v1_genomic.fna/target_genomes.txt --output GCF_003730195.1_ASM373019v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:21,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:21,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:21,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:21,409] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:21,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:21,410] [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
Halosimplex salinum	strain=YPL4	GCA_003730195.1	1710538	1710538	type	True	100.0	1675	1677	95	conclusive
Halosimplex pelagicum	strain=R2	GCA_013415905.1	869886	869886	type	True	84.6219	1082	1677	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	84.6132	1052	1677	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	84.494	1079	1677	95	below_threshold
Halosimplex carlsbadense	strain=2-9-1	GCA_000337455.1	171164	171164	type	True	84.2106	1067	1677	95	below_threshold
Halosimplex litoreum	strain=YGH94	GCA_016065055.1	1198301	1198301	type	True	83.8032	1006	1677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:21,412] [INFO] DFAST Taxonomy check result was written to GCF_003730195.1_ASM373019v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:21,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:21,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:21,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference/checkm_data
[2024-01-24 13:19:21,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:21,464] [INFO] Task started: CheckM
[2024-01-24 13:19:21,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003730195.1_ASM373019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003730195.1_ASM373019v1_genomic.fna/checkm_input GCF_003730195.1_ASM373019v1_genomic.fna/checkm_result
[2024-01-24 13:20:22,945] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:22,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:22,967] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:22,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:22,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003730195.1_ASM373019v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:22,968] [INFO] Task started: Blastn
[2024-01-24 13:20:22,968] [INFO] Running command: blastn -query GCF_003730195.1_ASM373019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bea087d-cdcb-4ab9-96cc-fc4876a9398d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003730195.1_ASM373019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:23,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:23,483] [INFO] Selected 6 target genomes.
[2024-01-24 13:20:23,483] [INFO] Target genome list was writen to GCF_003730195.1_ASM373019v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:23,494] [INFO] Task started: fastANI
[2024-01-24 13:20:23,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgecbf9348-0fc8-4017-83b9-7d9cdb4888ee/GCF_003730195.1_ASM373019v1_genomic.fna.gz --refList GCF_003730195.1_ASM373019v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003730195.1_ASM373019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:31,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:31,694] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:31,694] [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_003730195.1	s__Halosimplex salinum	100.0	1675	1677	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013415905.1	s__Halosimplex pelagicum	84.6623	1078	1677	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415885.1	s__Halosimplex rubrum	84.6426	1049	1677	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	84.4483	1082	1677	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337455.1	s__Halosimplex carlsbadense	84.2404	1063	1677	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023165.1	s__Halosimplex sp003023165	84.1741	585	1677	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	96.29	96.29	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:31,696] [INFO] GTDB search result was written to GCF_003730195.1_ASM373019v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:31,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:31,699] [INFO] DFAST_QC result json was written to GCF_003730195.1_ASM373019v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:31,699] [INFO] DFAST_QC completed!
[2024-01-24 13:20:31,699] [INFO] Total running time: 0h1m46s