[2024-01-25 18:49:05,652] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:05,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:05,653] [INFO] DQC Reference Directory: /var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference
[2024-01-25 18:49:06,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:06,773] [INFO] Task started: Prodigal
[2024-01-25 18:49:06,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg2911d3e3-8f80-4b84-bc80-ae2081f8e30b/GCF_000337895.1_ASM33789v1_genomic.fna.gz | prodigal -d GCF_000337895.1_ASM33789v1_genomic.fna/cds.fna -a GCF_000337895.1_ASM33789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:20,760] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:20,760] [INFO] Task started: HMMsearch
[2024-01-25 18:49:20,760] [INFO] Running command: hmmsearch --tblout GCF_000337895.1_ASM33789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference/reference_markers.hmm GCF_000337895.1_ASM33789v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:20,986] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:20,987] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2911d3e3-8f80-4b84-bc80-ae2081f8e30b/GCF_000337895.1_ASM33789v1_genomic.fna.gz]
[2024-01-25 18:49:21,017] [INFO] Query marker FASTA was written to GCF_000337895.1_ASM33789v1_genomic.fna/markers.fasta
[2024-01-25 18:49:21,017] [INFO] Task started: Blastn
[2024-01-25 18:49:21,018] [INFO] Running command: blastn -query GCF_000337895.1_ASM33789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference/reference_markers.fasta -out GCF_000337895.1_ASM33789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:21,504] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:21,507] [INFO] Selected 10 target genomes.
[2024-01-25 18:49:21,507] [INFO] Target genome list was writen to GCF_000337895.1_ASM33789v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:21,513] [INFO] Task started: fastANI
[2024-01-25 18:49:21,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg2911d3e3-8f80-4b84-bc80-ae2081f8e30b/GCF_000337895.1_ASM33789v1_genomic.fna.gz --refList GCF_000337895.1_ASM33789v1_genomic.fna/target_genomes.txt --output GCF_000337895.1_ASM33789v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:30,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:30,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:30,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:30,497] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:49:30,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:49:30,497] [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
Natronobacterium gregoryi	strain=SP2	GCA_000230715.3	44930	44930	type	True	82.6307	690	1135	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	82.5686	690	1135	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_000337655.1	44930	44930	type	True	82.5676	677	1135	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_002855455.1	44930	44930	type	True	82.501	671	1135	95	below_threshold
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	82.4359	746	1135	95	below_threshold
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	80.5994	633	1135	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	80.3188	603	1135	95	below_threshold
Haloterrigena turkmenica	strain=DSM 5511	GCA_000025325.1	62320	62320	type	True	80.3081	603	1135	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	80.1977	592	1135	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	80.0683	594	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:30,499] [INFO] DFAST Taxonomy check result was written to GCF_000337895.1_ASM33789v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:30,499] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:30,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:30,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference/checkm_data
[2024-01-25 18:49:30,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:30,539] [INFO] Task started: CheckM
[2024-01-25 18:49:30,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337895.1_ASM33789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337895.1_ASM33789v1_genomic.fna/checkm_input GCF_000337895.1_ASM33789v1_genomic.fna/checkm_result
[2024-01-25 18:50:10,347] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:10,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:10,368] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:10,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:10,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337895.1_ASM33789v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:10,369] [INFO] Task started: Blastn
[2024-01-25 18:50:10,369] [INFO] Running command: blastn -query GCF_000337895.1_ASM33789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcefc1a67-0033-431f-9ae6-17ce021439f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337895.1_ASM33789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:10,915] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:10,918] [INFO] Selected 9 target genomes.
[2024-01-25 18:50:10,919] [INFO] Target genome list was writen to GCF_000337895.1_ASM33789v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:10,925] [INFO] Task started: fastANI
[2024-01-25 18:50:10,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg2911d3e3-8f80-4b84-bc80-ae2081f8e30b/GCF_000337895.1_ASM33789v1_genomic.fna.gz --refList GCF_000337895.1_ASM33789v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337895.1_ASM33789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:19,808] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:19,815] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:19,815] [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_000337895.1	s__Halobiforma nitratireducens	100.0	1133	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000226975.2	s__Halobiforma lacisalsi	83.5098	809	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000230715.2	s__Natronobacterium gregoryi	82.6279	691	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	99.99	99.97	1.00	1.00	4	-
GCF_900104065.1	s__Natronobacterium texcoconense	82.4999	740	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	80.6202	632	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337495.1	s__Haloterrigena salina	80.3512	599	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025325.1	s__Haloterrigena turkmenica	80.2894	604	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	80.2476	569	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	80.0677	594	1135	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:19,817] [INFO] GTDB search result was written to GCF_000337895.1_ASM33789v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:19,817] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:19,820] [INFO] DFAST_QC result json was written to GCF_000337895.1_ASM33789v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:19,820] [INFO] DFAST_QC completed!
[2024-01-25 18:50:19,820] [INFO] Total running time: 0h1m14s