[2024-01-24 15:10:20,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference
[2024-01-24 15:10:22,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,719] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg6199ad97-8d9b-4971-a35b-51fa08d6a61d/GCF_025913575.1_ASM2591357v1_genomic.fna.gz | prodigal -d GCF_025913575.1_ASM2591357v1_genomic.fna/cds.fna -a GCF_025913575.1_ASM2591357v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:45,149] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:45,149] [INFO] Task started: HMMsearch
[2024-01-24 15:10:45,149] [INFO] Running command: hmmsearch --tblout GCF_025913575.1_ASM2591357v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference/reference_markers.hmm GCF_025913575.1_ASM2591357v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:45,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:45,397] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6199ad97-8d9b-4971-a35b-51fa08d6a61d/GCF_025913575.1_ASM2591357v1_genomic.fna.gz]
[2024-01-24 15:10:45,455] [INFO] Query marker FASTA was written to GCF_025913575.1_ASM2591357v1_genomic.fna/markers.fasta
[2024-01-24 15:10:45,456] [INFO] Task started: Blastn
[2024-01-24 15:10:45,456] [INFO] Running command: blastn -query GCF_025913575.1_ASM2591357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference/reference_markers.fasta -out GCF_025913575.1_ASM2591357v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:45,980] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:45,983] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:45,984] [INFO] Target genome list was writen to GCF_025913575.1_ASM2591357v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:45,991] [INFO] Task started: fastANI
[2024-01-24 15:10:45,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg6199ad97-8d9b-4971-a35b-51fa08d6a61d/GCF_025913575.1_ASM2591357v1_genomic.fna.gz --refList GCF_025913575.1_ASM2591357v1_genomic.fna/target_genomes.txt --output GCF_025913575.1_ASM2591357v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:54,319] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:54,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:54,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:54,332] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:10:54,332] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:10:54,333] [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
Halocatena pleomorpha	strain=SPP-AMP-1	GCA_003862495.1	1785090	1785090	type	True	77.2874	231	1318	95	below_threshold
Halalkalicoccus jeotgali	strain=B3	GCA_000337255.1	413810	413810	type	True	76.493	64	1318	95	below_threshold
Halomarina rubra	strain=ZS-47-S	GCA_023699475.1	2071873	2071873	type	True	76.4752	114	1318	95	below_threshold
Halalkalicoccus jeotgali	strain=B3	GCA_000196895.1	413810	413810	type	True	76.4731	65	1318	95	below_threshold
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	76.4446	98	1318	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	76.3426	116	1318	95	below_threshold
Haloarcula vallismortis	strain=DSM 3756	GCA_900106715.1	28442	28442	type	True	76.3318	70	1318	95	below_threshold
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	76.26	96	1318	95	below_threshold
Halomicroarcula amylolytica	strain=LR21	GCA_004681185.1	2562280	2562280	type	True	76.2122	80	1318	95	below_threshold
Haloarchaeobius litoreus	strain=GX1	GCA_024495425.1	755306	755306	type	True	76.1934	86	1318	95	below_threshold
Haloarcula vallismortis	strain=ATCC 29715	GCA_000337775.1	28442	28442	type	True	76.1812	68	1318	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	76.1521	86	1318	95	below_threshold
Haloprofundus marisrubri	strain=SB9	GCA_001469955.1	1514971	1514971	type	True	75.8444	80	1318	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:54,335] [INFO] DFAST Taxonomy check result was written to GCF_025913575.1_ASM2591357v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:54,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:54,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:54,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference/checkm_data
[2024-01-24 15:10:54,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:54,379] [INFO] Task started: CheckM
[2024-01-24 15:10:54,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025913575.1_ASM2591357v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025913575.1_ASM2591357v1_genomic.fna/checkm_input GCF_025913575.1_ASM2591357v1_genomic.fna/checkm_result
[2024-01-24 15:12:02,599] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:02,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:02,624] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:02,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:02,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025913575.1_ASM2591357v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:02,625] [INFO] Task started: Blastn
[2024-01-24 15:12:02,626] [INFO] Running command: blastn -query GCF_025913575.1_ASM2591357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19860815-509f-47fc-b9c0-3b1e90b6b6fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_025913575.1_ASM2591357v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:03,113] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:03,118] [INFO] Selected 12 target genomes.
[2024-01-24 15:12:03,118] [INFO] Target genome list was writen to GCF_025913575.1_ASM2591357v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:03,137] [INFO] Task started: fastANI
[2024-01-24 15:12:03,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg6199ad97-8d9b-4971-a35b-51fa08d6a61d/GCF_025913575.1_ASM2591357v1_genomic.fna.gz --refList GCF_025913575.1_ASM2591357v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025913575.1_ASM2591357v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:10,220] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:10,234] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:12:10,234] [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_003862495.1	s__Halomarina oriensis_A	77.2638	233	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103505.1	s__Haloarchaeobius iranensis	76.5425	64	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196895.1	s__Halalkalicoccus jeotgali	76.4731	65	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halalkalicoccaceae;g__Halalkalicoccus	95.0	99.99	99.98	1.00	1.00	3	-
GCF_003439925.1	s__Haloprofundus halophilus	76.242	97	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	98.76	98.76	0.93	0.93	2	-
GCF_000337355.1	s__Halorubrum kocurii	76.2222	64	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681185.1	s__Halomicroarcula amylolytica	76.2122	80	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337775.1	s__Haloarcula vallismortis	76.1812	68	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003675875.1	s__Halostella sp003675875	76.1521	86	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009741975.1	s__Halobacterium sp009741975	75.9912	55	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023565.1	s__Halostella sp003023565	75.9583	68	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469955.1	s__Haloprofundus marisrubri	75.8613	81	1318	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:10,242] [INFO] GTDB search result was written to GCF_025913575.1_ASM2591357v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:10,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:10,249] [INFO] DFAST_QC result json was written to GCF_025913575.1_ASM2591357v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:10,249] [INFO] DFAST_QC completed!
[2024-01-24 15:12:10,250] [INFO] Total running time: 0h1m50s