[2024-01-24 10:47:06,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference
[2024-01-24 10:47:12,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg34af9f33-6db7-4f5a-b8ac-385140fb4a6b/GCF_024362485.1_ASM2436248v1_genomic.fna.gz | prodigal -d GCF_024362485.1_ASM2436248v1_genomic.fna/cds.fna -a GCF_024362485.1_ASM2436248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:31,471] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:31,471] [INFO] Task started: HMMsearch
[2024-01-24 10:47:31,471] [INFO] Running command: hmmsearch --tblout GCF_024362485.1_ASM2436248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference/reference_markers.hmm GCF_024362485.1_ASM2436248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:31,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:31,732] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg34af9f33-6db7-4f5a-b8ac-385140fb4a6b/GCF_024362485.1_ASM2436248v1_genomic.fna.gz]
[2024-01-24 10:47:31,767] [INFO] Query marker FASTA was written to GCF_024362485.1_ASM2436248v1_genomic.fna/markers.fasta
[2024-01-24 10:47:31,768] [INFO] Task started: Blastn
[2024-01-24 10:47:31,768] [INFO] Running command: blastn -query GCF_024362485.1_ASM2436248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference/reference_markers.fasta -out GCF_024362485.1_ASM2436248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:32,364] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:32,367] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:32,367] [INFO] Target genome list was writen to GCF_024362485.1_ASM2436248v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:32,372] [INFO] Task started: fastANI
[2024-01-24 10:47:32,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg34af9f33-6db7-4f5a-b8ac-385140fb4a6b/GCF_024362485.1_ASM2436248v1_genomic.fna.gz --refList GCF_024362485.1_ASM2436248v1_genomic.fna/target_genomes.txt --output GCF_024362485.1_ASM2436248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:41,673] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:41,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:41,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:41,685] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:41,685] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:41,685] [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
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	79.728	625	1402	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	79.6778	654	1402	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	79.6665	652	1402	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	79.6071	633	1402	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	79.4247	677	1402	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.3432	609	1402	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.281	615	1402	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	79.2793	517	1402	95	below_threshold
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	79.2633	551	1402	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	79.116	646	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:41,687] [INFO] DFAST Taxonomy check result was written to GCF_024362485.1_ASM2436248v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:41,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:41,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:41,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference/checkm_data
[2024-01-24 10:47:41,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:41,733] [INFO] Task started: CheckM
[2024-01-24 10:47:41,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024362485.1_ASM2436248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024362485.1_ASM2436248v1_genomic.fna/checkm_input GCF_024362485.1_ASM2436248v1_genomic.fna/checkm_result
[2024-01-24 10:48:34,563] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:34,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,586] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:34,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:34,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024362485.1_ASM2436248v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:34,587] [INFO] Task started: Blastn
[2024-01-24 10:48:34,587] [INFO] Running command: blastn -query GCF_024362485.1_ASM2436248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg193f98e4-254b-4381-9c00-147f575f7d8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024362485.1_ASM2436248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:35,141] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:35,144] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:35,145] [INFO] Target genome list was writen to GCF_024362485.1_ASM2436248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:35,153] [INFO] Task started: fastANI
[2024-01-24 10:48:35,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg34af9f33-6db7-4f5a-b8ac-385140fb4a6b/GCF_024362485.1_ASM2436248v1_genomic.fna.gz --refList GCF_024362485.1_ASM2436248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024362485.1_ASM2436248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:45,860] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:45,870] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:45,870] [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
GCA_001564255.1	s__Tc-Br11-E2g1 sp001564255	80.361	383	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11-E2g1	95.0	99.14	99.14	0.76	0.76	2	-
GCF_000337695.1	s__Natronococcus jeotgali	79.7198	626	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCF_000226975.2	s__Halobiforma lacisalsi	79.6305	659	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000337675.1	s__Natronococcus amylolyticus	79.6213	630	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112205.1	s__Halobiforma haloterrestris	79.4452	674	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_017357405.1	s__KZCA124 sp017357405	79.4036	629	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__KZCA124	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017357105.1	s__Tc-Br11 sp017357105	79.3923	572	1402	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_900110455.1	s__Natrinema salifodinae	79.3623	608	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002494345.1	s__Natrinema ejinorense	79.3066	592	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_004217335.1	s__Natrinema hispanicum	79.2889	547	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013456555.1	s__Natrinema sp013456555	79.1847	566	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	79.1069	647	1402	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:45,872] [INFO] GTDB search result was written to GCF_024362485.1_ASM2436248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:45,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:45,876] [INFO] DFAST_QC result json was written to GCF_024362485.1_ASM2436248v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:45,876] [INFO] DFAST_QC completed!
[2024-01-24 10:48:45,876] [INFO] Total running time: 0h1m39s