[2024-01-25 18:15:05,539] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:05,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:05,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference
[2024-01-25 18:15:06,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:06,645] [INFO] Task started: Prodigal
[2024-01-25 18:15:06,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg61301dc6-5629-4fef-b9b5-ce31715e44bf/GCF_024494565.1_ASM2449456v1_genomic.fna.gz | prodigal -d GCF_024494565.1_ASM2449456v1_genomic.fna/cds.fna -a GCF_024494565.1_ASM2449456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:19,170] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:19,171] [INFO] Task started: HMMsearch
[2024-01-25 18:15:19,171] [INFO] Running command: hmmsearch --tblout GCF_024494565.1_ASM2449456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference/reference_markers.hmm GCF_024494565.1_ASM2449456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:19,401] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:19,402] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg61301dc6-5629-4fef-b9b5-ce31715e44bf/GCF_024494565.1_ASM2449456v1_genomic.fna.gz]
[2024-01-25 18:15:19,436] [INFO] Query marker FASTA was written to GCF_024494565.1_ASM2449456v1_genomic.fna/markers.fasta
[2024-01-25 18:15:19,437] [INFO] Task started: Blastn
[2024-01-25 18:15:19,437] [INFO] Running command: blastn -query GCF_024494565.1_ASM2449456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference/reference_markers.fasta -out GCF_024494565.1_ASM2449456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:19,937] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:19,941] [INFO] Selected 9 target genomes.
[2024-01-25 18:15:19,941] [INFO] Target genome list was writen to GCF_024494565.1_ASM2449456v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:19,948] [INFO] Task started: fastANI
[2024-01-25 18:15:19,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg61301dc6-5629-4fef-b9b5-ce31715e44bf/GCF_024494565.1_ASM2449456v1_genomic.fna.gz --refList GCF_024494565.1_ASM2449456v1_genomic.fna/target_genomes.txt --output GCF_024494565.1_ASM2449456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:30,449] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:30,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:30,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:30,456] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:30,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:30,457] [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 rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	100.0	1093	1141	95	conclusive
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	91.0212	762	1141	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	87.8314	712	1141	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	87.5476	718	1141	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	87.527	755	1141	95	below_threshold
Halorubrum salsamenti	strain=Y69	GCA_007671685.1	2583990	2583990	type	True	87.4706	725	1141	95	below_threshold
Halorubrum amylolyticum	strain=ZC67	GCA_004114995.1	2508724	2508724	type	True	87.3724	718	1141	95	below_threshold
Halorubrum halophilum	strain=B8	GCA_000739595.1	413816	413816	type	True	87.2074	756	1141	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	87.1819	709	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:30,458] [INFO] DFAST Taxonomy check result was written to GCF_024494565.1_ASM2449456v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:30,458] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:30,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:30,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference/checkm_data
[2024-01-25 18:15:30,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:30,495] [INFO] Task started: CheckM
[2024-01-25 18:15:30,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024494565.1_ASM2449456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024494565.1_ASM2449456v1_genomic.fna/checkm_input GCF_024494565.1_ASM2449456v1_genomic.fna/checkm_result
[2024-01-25 18:16:07,277] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:07,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:07,312] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:07,312] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:07,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024494565.1_ASM2449456v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:07,313] [INFO] Task started: Blastn
[2024-01-25 18:16:07,313] [INFO] Running command: blastn -query GCF_024494565.1_ASM2449456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d95e69-2aad-4dc0-a62c-a7d74316d62f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024494565.1_ASM2449456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:07,831] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:07,834] [INFO] Selected 8 target genomes.
[2024-01-25 18:16:07,834] [INFO] Target genome list was writen to GCF_024494565.1_ASM2449456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:07,841] [INFO] Task started: fastANI
[2024-01-25 18:16:07,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg61301dc6-5629-4fef-b9b5-ce31715e44bf/GCF_024494565.1_ASM2449456v1_genomic.fna.gz --refList GCF_024494565.1_ASM2449456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024494565.1_ASM2449456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:17,323] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:17,330] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:16:17,330] [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_001261915.1	s__Halorubrum sp001261915	93.0859	792	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671725.1	s__Halorubrum depositum	90.9754	764	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721435.2	s__Halorubrum sp003721435	90.3421	809	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252755.1	s__Halorubrum sp002252755	89.8988	774	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.78	98.49	0.85	0.82	5	-
GCF_000337375.1	s__Halorubrum lipolyticum	87.8191	710	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007671685.1	s__Halorubrum salsamenti	87.4706	725	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739595.1	s__Halorubrum halophilum	87.2092	755	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.11	98.11	0.88	0.88	2	-
GCF_900102375.1	s__Halorubrum xinjiangense	85.95	742	1141	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:17,331] [INFO] GTDB search result was written to GCF_024494565.1_ASM2449456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:17,333] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:17,336] [INFO] DFAST_QC result json was written to GCF_024494565.1_ASM2449456v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:17,336] [INFO] DFAST_QC completed!
[2024-01-25 18:16:17,336] [INFO] Total running time: 0h1m12s