[2024-01-24 11:27:04,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference
[2024-01-24 11:27:05,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,792] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgc317c483-06ca-4f52-9ef8-e3838d1ddf7c/GCF_013391085.1_ASM1339108v1_genomic.fna.gz | prodigal -d GCF_013391085.1_ASM1339108v1_genomic.fna/cds.fna -a GCF_013391085.1_ASM1339108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:21,392] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:21,393] [INFO] Task started: HMMsearch
[2024-01-24 11:27:21,393] [INFO] Running command: hmmsearch --tblout GCF_013391085.1_ASM1339108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference/reference_markers.hmm GCF_013391085.1_ASM1339108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:21,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:21,637] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc317c483-06ca-4f52-9ef8-e3838d1ddf7c/GCF_013391085.1_ASM1339108v1_genomic.fna.gz]
[2024-01-24 11:27:21,674] [INFO] Query marker FASTA was written to GCF_013391085.1_ASM1339108v1_genomic.fna/markers.fasta
[2024-01-24 11:27:21,674] [INFO] Task started: Blastn
[2024-01-24 11:27:21,674] [INFO] Running command: blastn -query GCF_013391085.1_ASM1339108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference/reference_markers.fasta -out GCF_013391085.1_ASM1339108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:22,212] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:22,215] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:22,216] [INFO] Target genome list was writen to GCF_013391085.1_ASM1339108v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:22,222] [INFO] Task started: fastANI
[2024-01-24 11:27:22,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgc317c483-06ca-4f52-9ef8-e3838d1ddf7c/GCF_013391085.1_ASM1339108v1_genomic.fna.gz --refList GCF_013391085.1_ASM1339108v1_genomic.fna/target_genomes.txt --output GCF_013391085.1_ASM1339108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:29,987] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:29,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:29,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:30,003] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:30,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:30,004] [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
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	100.0	1067	1070	95	conclusive
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	81.7282	634	1070	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	81.2816	649	1070	95	below_threshold
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	79.4932	425	1070	95	below_threshold
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	78.9183	387	1070	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.066	399	1070	95	below_threshold
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	77.8519	350	1070	95	below_threshold
Haloglomus irregulare	strain=F16-60	GCA_007421925.1	2234134	2234134	type	True	77.7948	358	1070	95	below_threshold
Halapricum salinum	strain=CBA1105	GCA_004799665.1	1457250	1457250	type	True	77.6221	257	1070	95	below_threshold
Halapricum salinum	strain=CBA1105	GCA_000755225.1	1457250	1457250	type	True	77.5864	262	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,006] [INFO] DFAST Taxonomy check result was written to GCF_013391085.1_ASM1339108v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:30,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:30,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:30,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference/checkm_data
[2024-01-24 11:27:30,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:30,043] [INFO] Task started: CheckM
[2024-01-24 11:27:30,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013391085.1_ASM1339108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013391085.1_ASM1339108v1_genomic.fna/checkm_input GCF_013391085.1_ASM1339108v1_genomic.fna/checkm_result
[2024-01-24 11:28:14,169] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:14,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:14,200] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:14,201] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:14,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013391085.1_ASM1339108v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:14,202] [INFO] Task started: Blastn
[2024-01-24 11:28:14,202] [INFO] Running command: blastn -query GCF_013391085.1_ASM1339108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ecdda2f-c763-4727-9126-75836a8facbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_013391085.1_ASM1339108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:14,762] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:14,766] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:14,766] [INFO] Target genome list was writen to GCF_013391085.1_ASM1339108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:14,775] [INFO] Task started: fastANI
[2024-01-24 11:28:14,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgc317c483-06ca-4f52-9ef8-e3838d1ddf7c/GCF_013391085.1_ASM1339108v1_genomic.fna.gz --refList GCF_013391085.1_ASM1339108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013391085.1_ASM1339108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:21,175] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:21,194] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:21,194] [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_013391085.1	s__Natronomonas halophila	100.0	1062	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013391635.1	s__Natronomonas gomsonensis	81.8036	627	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741925.1	s__Natronomonas sp009741925	81.7884	609	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018609665.1	s__Natronomonas sp018609665	80.0317	428	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020965.1	s__Natronomonas sp003020965	79.7232	488	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021325.1	s__Natronomonas sp003021325	79.552	329	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026045.1	s__Natronomonas pharaonis	79.4538	430	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023535.1	s__Natronomonas sp003023535	79.3465	337	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839515.1	s__Natronomonas sp013839515	78.826	360	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.6968	273	1070	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 11:28:21,196] [INFO] GTDB search result was written to GCF_013391085.1_ASM1339108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:21,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:21,200] [INFO] DFAST_QC result json was written to GCF_013391085.1_ASM1339108v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:21,200] [INFO] DFAST_QC completed!
[2024-01-24 11:28:21,201] [INFO] Total running time: 0h1m17s