[2024-01-24 11:50:49,640] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,643] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference
[2024-01-24 11:50:50,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,897] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg56f07787-8693-4bb8-b852-0907fe853db7/GCF_024464185.1_ASM2446418v1_genomic.fna.gz | prodigal -d GCF_024464185.1_ASM2446418v1_genomic.fna/cds.fna -a GCF_024464185.1_ASM2446418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:10,548] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:10,548] [INFO] Task started: HMMsearch
[2024-01-24 11:51:10,548] [INFO] Running command: hmmsearch --tblout GCF_024464185.1_ASM2446418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference/reference_markers.hmm GCF_024464185.1_ASM2446418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:10,801] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:10,803] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg56f07787-8693-4bb8-b852-0907fe853db7/GCF_024464185.1_ASM2446418v1_genomic.fna.gz]
[2024-01-24 11:51:10,838] [INFO] Query marker FASTA was written to GCF_024464185.1_ASM2446418v1_genomic.fna/markers.fasta
[2024-01-24 11:51:10,839] [INFO] Task started: Blastn
[2024-01-24 11:51:10,839] [INFO] Running command: blastn -query GCF_024464185.1_ASM2446418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference/reference_markers.fasta -out GCF_024464185.1_ASM2446418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:11,371] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:11,375] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:11,375] [INFO] Target genome list was writen to GCF_024464185.1_ASM2446418v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:11,381] [INFO] Task started: fastANI
[2024-01-24 11:51:11,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f07787-8693-4bb8-b852-0907fe853db7/GCF_024464185.1_ASM2446418v1_genomic.fna.gz --refList GCF_024464185.1_ASM2446418v1_genomic.fna/target_genomes.txt --output GCF_024464185.1_ASM2446418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:23,456] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:23,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:23,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:23,473] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:23,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:23,473] [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 salinus	strain=YC82	GCA_024464185.1	1198298	1198298	type	True	100.0	1276	1276	95	conclusive
Haloarchaeobius litoreus	strain=GX1	GCA_024495425.1	755306	755306	type	True	91.1888	1032	1276	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	79.3437	556	1276	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	79.3297	554	1276	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	78.7468	573	1276	95	below_threshold
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	78.3779	489	1276	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	78.3399	490	1276	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	78.2691	464	1276	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	78.213	468	1276	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	78.1786	478	1276	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.114	520	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:23,475] [INFO] DFAST Taxonomy check result was written to GCF_024464185.1_ASM2446418v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:23,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:23,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:23,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference/checkm_data
[2024-01-24 11:51:23,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:23,515] [INFO] Task started: CheckM
[2024-01-24 11:51:23,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024464185.1_ASM2446418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024464185.1_ASM2446418v1_genomic.fna/checkm_input GCF_024464185.1_ASM2446418v1_genomic.fna/checkm_result
[2024-01-24 11:52:16,593] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:16,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,617] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:16,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:16,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024464185.1_ASM2446418v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:16,618] [INFO] Task started: Blastn
[2024-01-24 11:52:16,618] [INFO] Running command: blastn -query GCF_024464185.1_ASM2446418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc210ef3-baa7-44df-b58f-4c5ecad81172/dqc_reference/reference_markers_gtdb.fasta -out GCF_024464185.1_ASM2446418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,142] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,146] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:17,146] [INFO] Target genome list was writen to GCF_024464185.1_ASM2446418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:17,157] [INFO] Task started: fastANI
[2024-01-24 11:52:17,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f07787-8693-4bb8-b852-0907fe853db7/GCF_024464185.1_ASM2446418v1_genomic.fna.gz --refList GCF_024464185.1_ASM2446418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024464185.1_ASM2446418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:27,507] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:27,529] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:27,530] [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	89.3996	957	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	79.3214	555	1276	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_011440375.1	s__Halorubellus sp011440375	79.2207	595	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halorubellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	78.7538	571	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013391105.1	s__Natronomonas salina	78.61	465	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765805.1	s__Halorussus sp004765805	78.3994	485	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	78.3025	458	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	78.211	466	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	78.1746	473	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	78.115	431	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_004698125.1	s__Halosimplex halophilum	78.1132	523	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.7873	349	1276	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	-
GCA_003021325.1	s__Natronomonas sp003021325	77.16	253	1276	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:27,532] [INFO] GTDB search result was written to GCF_024464185.1_ASM2446418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:27,533] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:27,538] [INFO] DFAST_QC result json was written to GCF_024464185.1_ASM2446418v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:27,538] [INFO] DFAST_QC completed!
[2024-01-24 11:52:27,539] [INFO] Total running time: 0h1m38s