[2024-01-25 18:40:35,787] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:35,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:35,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference
[2024-01-25 18:40:36,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:36,962] [INFO] Task started: Prodigal
[2024-01-25 18:40:36,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1320f8d-47d8-4e02-8e65-9851a7b5b48e/GCF_000455345.1_Halgo_genomic.fna.gz | prodigal -d GCF_000455345.1_Halgo_genomic.fna/cds.fna -a GCF_000455345.1_Halgo_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:51,699] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:51,699] [INFO] Task started: HMMsearch
[2024-01-25 18:40:51,699] [INFO] Running command: hmmsearch --tblout GCF_000455345.1_Halgo_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference/reference_markers.hmm GCF_000455345.1_Halgo_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:51,926] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:51,927] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd1320f8d-47d8-4e02-8e65-9851a7b5b48e/GCF_000455345.1_Halgo_genomic.fna.gz]
[2024-01-25 18:40:51,959] [INFO] Query marker FASTA was written to GCF_000455345.1_Halgo_genomic.fna/markers.fasta
[2024-01-25 18:40:51,959] [INFO] Task started: Blastn
[2024-01-25 18:40:51,959] [INFO] Running command: blastn -query GCF_000455345.1_Halgo_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference/reference_markers.fasta -out GCF_000455345.1_Halgo_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:52,463] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:52,465] [INFO] Selected 12 target genomes.
[2024-01-25 18:40:52,466] [INFO] Target genome list was writen to GCF_000455345.1_Halgo_genomic.fna/target_genomes.txt
[2024-01-25 18:40:52,470] [INFO] Task started: fastANI
[2024-01-25 18:40:52,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1320f8d-47d8-4e02-8e65-9851a7b5b48e/GCF_000455345.1_Halgo_genomic.fna.gz --refList GCF_000455345.1_Halgo_genomic.fna/target_genomes.txt --output GCF_000455345.1_Halgo_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:06,252] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:06,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:06,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:06,261] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:06,261] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:06,262] [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
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	100.0	1299	1300	95	conclusive
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	82.3351	798	1300	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	82.275	808	1300	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	82.0205	772	1300	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	81.8751	791	1300	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	81.8609	791	1300	95	below_threshold
Haloterrigena turkmenica	strain=DSM 5511	GCA_000025325.1	62320	62320	type	True	81.6773	810	1300	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	81.4516	798	1300	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000337635.1	69525	69525	type	True	81.223	715	1300	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000230735.3	69525	69525	type	True	81.1706	737	1300	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	81.0533	762	1300	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	80.9951	768	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:06,265] [INFO] DFAST Taxonomy check result was written to GCF_000455345.1_Halgo_genomic.fna/tc_result.tsv
[2024-01-25 18:41:06,265] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:06,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:06,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference/checkm_data
[2024-01-25 18:41:06,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:06,316] [INFO] Task started: CheckM
[2024-01-25 18:41:06,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000455345.1_Halgo_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000455345.1_Halgo_genomic.fna/checkm_input GCF_000455345.1_Halgo_genomic.fna/checkm_result
[2024-01-25 18:41:46,508] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:46,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:46,530] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:46,530] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:46,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000455345.1_Halgo_genomic.fna/markers.fasta)
[2024-01-25 18:41:46,531] [INFO] Task started: Blastn
[2024-01-25 18:41:46,531] [INFO] Running command: blastn -query GCF_000455345.1_Halgo_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2cb82d4-a284-485b-adaf-fa13ab56d05f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000455345.1_Halgo_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:47,034] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:47,037] [INFO] Selected 12 target genomes.
[2024-01-25 18:41:47,037] [INFO] Target genome list was writen to GCF_000455345.1_Halgo_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:47,043] [INFO] Task started: fastANI
[2024-01-25 18:41:47,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1320f8d-47d8-4e02-8e65-9851a7b5b48e/GCF_000455345.1_Halgo_genomic.fna.gz --refList GCF_000455345.1_Halgo_genomic.fna/target_genomes_gtdb.txt --output GCF_000455345.1_Halgo_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:59,871] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:59,879] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:59,880] [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_000455345.1	s__Halopiger_A goleimassiliensis	100.0	1299	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610195.1	s__Halopiger aswanensis	82.3838	797	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	82.3326	798	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	81.9985	831	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000337495.1	s__Haloterrigena salina	81.8927	788	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	81.6629	555	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000690595.2	s__Natrinema mahii	81.5417	722	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	81.4717	795	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000230735.2	s__Natrinema pellirubrum	81.1796	734	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.7501	99.98	99.98	1.00	1.00	2	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	81.1717	749	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	81.0254	766	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100335.1	s__Natronorubrum texcoconense	80.8369	758	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:59,881] [INFO] GTDB search result was written to GCF_000455345.1_Halgo_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:59,882] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:59,885] [INFO] DFAST_QC result json was written to GCF_000455345.1_Halgo_genomic.fna/dqc_result.json
[2024-01-25 18:41:59,885] [INFO] DFAST_QC completed!
[2024-01-25 18:41:59,885] [INFO] Total running time: 0h1m24s