[2024-01-25 20:11:35,402] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:35,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:35,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference
[2024-01-25 20:11:36,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:36,612] [INFO] Task started: Prodigal
[2024-01-25 20:11:36,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg54b8bcf7-f77d-4383-8b0f-0662f606b564/GCF_001693735.1_ASM169373v1_genomic.fna.gz | prodigal -d GCF_001693735.1_ASM169373v1_genomic.fna/cds.fna -a GCF_001693735.1_ASM169373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:41,051] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:41,051] [INFO] Task started: HMMsearch
[2024-01-25 20:11:41,051] [INFO] Running command: hmmsearch --tblout GCF_001693735.1_ASM169373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference/reference_markers.hmm GCF_001693735.1_ASM169373v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:41,264] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:41,265] [INFO] Found 6/6 markers.
[2024-01-25 20:11:41,293] [INFO] Query marker FASTA was written to GCF_001693735.1_ASM169373v1_genomic.fna/markers.fasta
[2024-01-25 20:11:41,293] [INFO] Task started: Blastn
[2024-01-25 20:11:41,293] [INFO] Running command: blastn -query GCF_001693735.1_ASM169373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference/reference_markers.fasta -out GCF_001693735.1_ASM169373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:41,839] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:41,843] [INFO] Selected 16 target genomes.
[2024-01-25 20:11:41,843] [INFO] Target genome list was writen to GCF_001693735.1_ASM169373v1_genomic.fna/target_genomes.txt
[2024-01-25 20:11:41,871] [INFO] Task started: fastANI
[2024-01-25 20:11:41,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg54b8bcf7-f77d-4383-8b0f-0662f606b564/GCF_001693735.1_ASM169373v1_genomic.fna.gz --refList GCF_001693735.1_ASM169373v1_genomic.fna/target_genomes.txt --output GCF_001693735.1_ASM169373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:11:49,656] [INFO] Task succeeded: fastANI
[2024-01-25 20:11:49,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:11:49,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:11:49,663] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:11:49,663] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:11:49,663] [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
Orenia metallireducens	strain=Z6	GCA_001693735.1	1413210	1413210	type	True	99.9982	1148	1150	95	conclusive
Orenia marismortui	strain=DSM 5156	GCA_000379025.1	46469	46469	type	True	79.4699	477	1150	95	below_threshold
Halonatronum saccharophilum	strain=DSM 13868	GCA_000517025.1	150060	150060	type	True	77.4563	190	1150	95	below_threshold
Halobacteroides halobius	strain=DSM 5150	GCA_000328625.1	42422	42422	type	True	76.7579	153	1150	95	below_threshold
Natroniella sulfidigena	strain=AHT3	GCA_023223645.1	723921	723921	type	True	76.5972	125	1150	95	below_threshold
Natroniella acetigena	strain=Z-7937	GCA_023227745.1	52004	52004	type	True	76.3617	111	1150	95	below_threshold
Halanaerobacter jeridensis	strain=DSM 23230	GCA_016908315.1	706427	706427	type	True	76.0624	107	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:11:49,665] [INFO] DFAST Taxonomy check result was written to GCF_001693735.1_ASM169373v1_genomic.fna/tc_result.tsv
[2024-01-25 20:11:49,665] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:11:49,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:11:49,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference/checkm_data
[2024-01-25 20:11:49,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:11:49,701] [INFO] Task started: CheckM
[2024-01-25 20:11:49,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001693735.1_ASM169373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001693735.1_ASM169373v1_genomic.fna/checkm_input GCF_001693735.1_ASM169373v1_genomic.fna/checkm_result
[2024-01-25 20:12:08,579] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:08,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:08,602] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:08,602] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:08,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001693735.1_ASM169373v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:08,603] [INFO] Task started: Blastn
[2024-01-25 20:12:08,603] [INFO] Running command: blastn -query GCF_001693735.1_ASM169373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86d56cda-82cc-4a62-b4d8-56b3bdcd462d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001693735.1_ASM169373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:09,304] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:09,307] [INFO] Selected 11 target genomes.
[2024-01-25 20:12:09,307] [INFO] Target genome list was writen to GCF_001693735.1_ASM169373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:09,322] [INFO] Task started: fastANI
[2024-01-25 20:12:09,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg54b8bcf7-f77d-4383-8b0f-0662f606b564/GCF_001693735.1_ASM169373v1_genomic.fna.gz --refList GCF_001693735.1_ASM169373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001693735.1_ASM169373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:15,847] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:15,853] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:15,853] [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_001693735.1	s__Orenia metallireducens	99.9982	1148	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Orenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003001995.1	s__Orenia metallireducens_B	86.6002	869	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Orenia	95.0	99.78	99.78	0.98	0.98	2	-
GCF_000379025.1	s__Orenia marismortui	79.4774	477	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Orenia	95.0	96.95	96.95	0.88	0.88	2	-
GCF_000517025.1	s__Halonatronum saccharophilum	77.5044	190	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halonatronum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328625.1	s__Halobacteroides halobius	76.7292	155	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114655.1	s__Frackibacter sp900114655	76.4584	84	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Frackibacter	95.0	99.43	98.34	0.95	0.87	4	-
GCF_016908315.1	s__Halanaerobacter jeridensis	76.0624	107	1150	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:15,854] [INFO] GTDB search result was written to GCF_001693735.1_ASM169373v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:15,855] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:15,862] [INFO] DFAST_QC result json was written to GCF_001693735.1_ASM169373v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:15,862] [INFO] DFAST_QC completed!
[2024-01-25 20:12:15,862] [INFO] Total running time: 0h0m40s