[2024-01-24 11:26:10,857] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:10,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:10,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference
[2024-01-24 11:26:12,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:12,150] [INFO] Task started: Prodigal
[2024-01-24 11:26:12,150] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd8bfefd-6ecb-4b76-be48-b53905cc43a3/GCF_024495425.1_ASM2449542v1_genomic.fna.gz | prodigal -d GCF_024495425.1_ASM2449542v1_genomic.fna/cds.fna -a GCF_024495425.1_ASM2449542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:33,801] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:33,802] [INFO] Task started: HMMsearch
[2024-01-24 11:26:33,802] [INFO] Running command: hmmsearch --tblout GCF_024495425.1_ASM2449542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference/reference_markers.hmm GCF_024495425.1_ASM2449542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:34,090] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:34,091] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfd8bfefd-6ecb-4b76-be48-b53905cc43a3/GCF_024495425.1_ASM2449542v1_genomic.fna.gz]
[2024-01-24 11:26:34,128] [INFO] Query marker FASTA was written to GCF_024495425.1_ASM2449542v1_genomic.fna/markers.fasta
[2024-01-24 11:26:34,128] [INFO] Task started: Blastn
[2024-01-24 11:26:34,128] [INFO] Running command: blastn -query GCF_024495425.1_ASM2449542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference/reference_markers.fasta -out GCF_024495425.1_ASM2449542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:34,686] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:34,690] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:34,690] [INFO] Target genome list was writen to GCF_024495425.1_ASM2449542v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:34,696] [INFO] Task started: fastANI
[2024-01-24 11:26:34,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8bfefd-6ecb-4b76-be48-b53905cc43a3/GCF_024495425.1_ASM2449542v1_genomic.fna.gz --refList GCF_024495425.1_ASM2449542v1_genomic.fna/target_genomes.txt --output GCF_024495425.1_ASM2449542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:45,384] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:45,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:45,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:45,395] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:45,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:45,396] [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
Haloarchaeobius litoreus	strain=GX1	GCA_024495425.1	755306	755306	type	True	100.0	1347	1347	95	conclusive
Haloarchaeobius salinus	strain=YC82	GCA_024464185.1	1198298	1198298	type	True	91.08	1060	1347	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	79.1085	576	1347	95	below_threshold
Halorussus litoreus	strain=HD8-51	GCA_003382685.1	1710536	1710536	type	True	78.4809	470	1347	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	78.4762	482	1347	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	78.3433	476	1347	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	78.3227	453	1347	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.2845	479	1347	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	78.1586	457	1347	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	78.133	472	1347	95	below_threshold
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	78.0847	503	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:45,410] [INFO] DFAST Taxonomy check result was written to GCF_024495425.1_ASM2449542v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:45,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:45,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:45,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference/checkm_data
[2024-01-24 11:26:45,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:45,456] [INFO] Task started: CheckM
[2024-01-24 11:26:45,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024495425.1_ASM2449542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024495425.1_ASM2449542v1_genomic.fna/checkm_input GCF_024495425.1_ASM2449542v1_genomic.fna/checkm_result
[2024-01-24 11:27:42,480] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:42,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:42,531] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:42,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:42,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024495425.1_ASM2449542v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:42,532] [INFO] Task started: Blastn
[2024-01-24 11:27:42,533] [INFO] Running command: blastn -query GCF_024495425.1_ASM2449542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7289b054-be49-4c9b-a062-01c1c2c5961d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024495425.1_ASM2449542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:43,056] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:43,060] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:43,060] [INFO] Target genome list was writen to GCF_024495425.1_ASM2449542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:43,068] [INFO] Task started: fastANI
[2024-01-24 11:27:43,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8bfefd-6ecb-4b76-be48-b53905cc43a3/GCF_024495425.1_ASM2449542v1_genomic.fna.gz --refList GCF_024495425.1_ASM2449542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024495425.1_ASM2449542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:54,129] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:54,143] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:54,143] [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_900103505.1	s__Haloarchaeobius iranensis	89.4432	982	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440375.1	s__Halorubellus sp011440375	79.186	597	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halorubellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	79.0871	579	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119195.1	s__Haloarcula salina	78.515	476	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003382685.1	s__Halorussus litoreus	78.4606	472	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.3274	473	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	78.3079	441	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	78.1342	472	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	78.1086	464	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765805.1	s__Halorussus sp004765805	78.0839	504	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118325.1	s__Halorientalis sp004118325	77.5343	406	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.464	339	1347	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:54,145] [INFO] GTDB search result was written to GCF_024495425.1_ASM2449542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:54,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:54,149] [INFO] DFAST_QC result json was written to GCF_024495425.1_ASM2449542v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:54,149] [INFO] DFAST_QC completed!
[2024-01-24 11:27:54,149] [INFO] Total running time: 0h1m43s