[2024-01-24 12:13:05,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:05,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:05,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference
[2024-01-24 12:13:06,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:06,633] [INFO] Task started: Prodigal
[2024-01-24 12:13:06,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg644bc91a-a6f5-49ea-bfcf-5e91e35892c9/GCF_008245225.1_ASM824522v1_genomic.fna.gz | prodigal -d GCF_008245225.1_ASM824522v1_genomic.fna/cds.fna -a GCF_008245225.1_ASM824522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:25,378] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:25,379] [INFO] Task started: HMMsearch
[2024-01-24 12:13:25,379] [INFO] Running command: hmmsearch --tblout GCF_008245225.1_ASM824522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference/reference_markers.hmm GCF_008245225.1_ASM824522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:25,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:25,584] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg644bc91a-a6f5-49ea-bfcf-5e91e35892c9/GCF_008245225.1_ASM824522v1_genomic.fna.gz]
[2024-01-24 12:13:25,616] [INFO] Query marker FASTA was written to GCF_008245225.1_ASM824522v1_genomic.fna/markers.fasta
[2024-01-24 12:13:25,616] [INFO] Task started: Blastn
[2024-01-24 12:13:25,617] [INFO] Running command: blastn -query GCF_008245225.1_ASM824522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference/reference_markers.fasta -out GCF_008245225.1_ASM824522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:26,128] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:26,132] [INFO] Selected 13 target genomes.
[2024-01-24 12:13:26,133] [INFO] Target genome list was writen to GCF_008245225.1_ASM824522v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:26,139] [INFO] Task started: fastANI
[2024-01-24 12:13:26,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg644bc91a-a6f5-49ea-bfcf-5e91e35892c9/GCF_008245225.1_ASM824522v1_genomic.fna.gz --refList GCF_008245225.1_ASM824522v1_genomic.fna/target_genomes.txt --output GCF_008245225.1_ASM824522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:37,283] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:37,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:37,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:37,294] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:13:37,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:13:37,295] [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
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	80.4951	720	1357	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	80.3615	699	1357	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	80.2484	693	1357	95	below_threshold
Natrarchaeobius halalkaliphilus	strain=AArcht-Sl	GCA_003841485.1	1679091	1679091	type	True	80.2432	621	1357	95	below_threshold
Halopiger djelfimassiliensis	strain=IIH2	GCA_000455365.1	1293047	1293047	type	True	80.1523	665	1357	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	80.1495	647	1357	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	80.012	622	1357	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.9567	622	1357	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	79.9272	605	1357	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	79.8988	666	1357	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	79.8811	684	1357	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	79.6805	542	1357	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	79.5819	606	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:37,298] [INFO] DFAST Taxonomy check result was written to GCF_008245225.1_ASM824522v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:37,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:37,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:37,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference/checkm_data
[2024-01-24 12:13:37,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:37,339] [INFO] Task started: CheckM
[2024-01-24 12:13:37,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008245225.1_ASM824522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008245225.1_ASM824522v1_genomic.fna/checkm_input GCF_008245225.1_ASM824522v1_genomic.fna/checkm_result
[2024-01-24 12:14:28,654] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:28,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:28,678] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:28,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:28,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008245225.1_ASM824522v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:28,679] [INFO] Task started: Blastn
[2024-01-24 12:14:28,679] [INFO] Running command: blastn -query GCF_008245225.1_ASM824522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a44cfb8-7de5-4d59-b5e9-6d2a680fe8d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008245225.1_ASM824522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:29,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:29,174] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:29,174] [INFO] Target genome list was writen to GCF_008245225.1_ASM824522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:29,182] [INFO] Task started: fastANI
[2024-01-24 12:14:29,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg644bc91a-a6f5-49ea-bfcf-5e91e35892c9/GCF_008245225.1_ASM824522v1_genomic.fna.gz --refList GCF_008245225.1_ASM824522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008245225.1_ASM824522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:40,784] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:40,795] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:40,795] [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_008245225.1	s__Natrarchaeobius swarupiae	100.0	1354	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	96.49	96.49	0.86	0.86	2	conclusive
GCF_003841505.1	s__Natrarchaeobius chitinivorans	82.3661	843	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003841465.1	s__Natrarchaeobius chitinivorans_A	81.1563	792	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	80.374	697	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	80.2671	606	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	80.1519	692	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_900110455.1	s__Natrinema salifodinae	79.9621	621	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000337195.1	s__Natrinema versiforme	79.9278	605	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337495.1	s__Haloterrigena salina	79.9054	680	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	79.8947	667	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_002494345.1	s__Natrinema ejinorense	79.8281	621	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_003430825.1	s__Natrarchaeobaculum sulfurireducens	79.636	640	1357	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	99.22	99.22	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:40,796] [INFO] GTDB search result was written to GCF_008245225.1_ASM824522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:40,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:40,801] [INFO] DFAST_QC result json was written to GCF_008245225.1_ASM824522v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:40,801] [INFO] DFAST_QC completed!
[2024-01-24 12:14:40,801] [INFO] Total running time: 0h1m35s