[2024-01-24 13:01:19,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,169] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference
[2024-01-24 13:01:20,414] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,415] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,415] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7b3c9c6-fce7-4231-b279-eeeae80a9956/GCF_023093535.1_ASM2309353v1_genomic.fna.gz | prodigal -d GCF_023093535.1_ASM2309353v1_genomic.fna/cds.fna -a GCF_023093535.1_ASM2309353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:37,431] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:37,432] [INFO] Task started: HMMsearch
[2024-01-24 13:01:37,432] [INFO] Running command: hmmsearch --tblout GCF_023093535.1_ASM2309353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference/reference_markers.hmm GCF_023093535.1_ASM2309353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:37,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:37,663] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb7b3c9c6-fce7-4231-b279-eeeae80a9956/GCF_023093535.1_ASM2309353v1_genomic.fna.gz]
[2024-01-24 13:01:37,701] [INFO] Query marker FASTA was written to GCF_023093535.1_ASM2309353v1_genomic.fna/markers.fasta
[2024-01-24 13:01:37,701] [INFO] Task started: Blastn
[2024-01-24 13:01:37,702] [INFO] Running command: blastn -query GCF_023093535.1_ASM2309353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference/reference_markers.fasta -out GCF_023093535.1_ASM2309353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:38,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:38,238] [INFO] Selected 9 target genomes.
[2024-01-24 13:01:38,238] [INFO] Target genome list was writen to GCF_023093535.1_ASM2309353v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:38,250] [INFO] Task started: fastANI
[2024-01-24 13:01:38,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7b3c9c6-fce7-4231-b279-eeeae80a9956/GCF_023093535.1_ASM2309353v1_genomic.fna.gz --refList GCF_023093535.1_ASM2309353v1_genomic.fna/target_genomes.txt --output GCF_023093535.1_ASM2309353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:46,750] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:46,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:46,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:46,765] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:46,766] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:46,766] [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
Halovivax limisalsi	strain=IBRC-M 10022	GCA_023093535.1	1453760	1453760	type	True	100.0	1298	1298	95	conclusive
Halovivax cerinus	strain=IBRC-M 10256	GCA_024498195.1	1487865	1487865	type	True	81.7418	722	1298	95	below_threshold
Halovivax asiaticus	strain=JCM 14624	GCA_000337515.1	332953	332953	type	True	81.2178	660	1298	95	below_threshold
Halovivax ruber	strain=XH-70	GCA_000328525.1	387341	387341	type	True	81.1557	657	1298	95	below_threshold
Haloterrigena turkmenica	strain=DSM 5511	GCA_000025325.1	62320	62320	type	True	78.9427	545	1298	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	78.6548	508	1298	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	78.2746	441	1298	95	below_threshold
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	77.4713	366	1298	95	below_threshold
Halobaculum roseum	strain=CGMCC 1.15501	GCA_019880245.1	2175149	2175149	type	True	77.3392	398	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:46,768] [INFO] DFAST Taxonomy check result was written to GCF_023093535.1_ASM2309353v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:46,769] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:46,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:46,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference/checkm_data
[2024-01-24 13:01:46,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:46,810] [INFO] Task started: CheckM
[2024-01-24 13:01:46,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023093535.1_ASM2309353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023093535.1_ASM2309353v1_genomic.fna/checkm_input GCF_023093535.1_ASM2309353v1_genomic.fna/checkm_result
[2024-01-24 13:02:34,033] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:34,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,064] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:34,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:34,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023093535.1_ASM2309353v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:34,066] [INFO] Task started: Blastn
[2024-01-24 13:02:34,066] [INFO] Running command: blastn -query GCF_023093535.1_ASM2309353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b62a84-3931-4ae4-9e53-ff4c706b372b/dqc_reference/reference_markers_gtdb.fasta -out GCF_023093535.1_ASM2309353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:34,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:34,594] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:34,594] [INFO] Target genome list was writen to GCF_023093535.1_ASM2309353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:34,608] [INFO] Task started: fastANI
[2024-01-24 13:02:34,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7b3c9c6-fce7-4231-b279-eeeae80a9956/GCF_023093535.1_ASM2309353v1_genomic.fna.gz --refList GCF_023093535.1_ASM2309353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023093535.1_ASM2309353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:44,388] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:44,410] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:44,411] [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_000337515.1	s__Halovivax asiaticus	81.1785	664	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328525.1	s__Halovivax ruber	81.1447	657	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119345.1	s__Halovivax sp007119345	79.7934	550	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025325.1	s__Haloterrigena turkmenica	78.8997	551	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017357105.1	s__Tc-Br11 sp017357105	78.7759	469	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	78.7357	532	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122205.1	s__Natronococcus sp008122205	78.6541	509	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	78.6259	506	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357405.1	s__KZCA124 sp017357405	78.4772	519	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__KZCA124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	78.2441	444	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003342675.1	s__Haloplanus rubicundus	77.1265	338	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	98.71	98.71	0.88	0.88	2	-
GCF_900129775.1	s__Halobaculum gomorrense	77.1215	340	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,413] [INFO] GTDB search result was written to GCF_023093535.1_ASM2309353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:44,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:44,417] [INFO] DFAST_QC result json was written to GCF_023093535.1_ASM2309353v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:44,417] [INFO] DFAST_QC completed!
[2024-01-24 13:02:44,417] [INFO] Total running time: 0h1m25s