[2024-01-24 13:28:29,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference
[2024-01-24 13:28:30,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,432] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bff0cc5-7feb-4d4b-babb-7c13bd02fab0/GCF_000021985.1_ASM2198v1_genomic.fna.gz | prodigal -d GCF_000021985.1_ASM2198v1_genomic.fna/cds.fna -a GCF_000021985.1_ASM2198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,455] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,456] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,456] [INFO] Running command: hmmsearch --tblout GCF_000021985.1_ASM2198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference/reference_markers.hmm GCF_000021985.1_ASM2198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,697] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,699] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,730] [INFO] Query marker FASTA was written to GCF_000021985.1_ASM2198v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,730] [INFO] Task started: Blastn
[2024-01-24 13:28:41,730] [INFO] Running command: blastn -query GCF_000021985.1_ASM2198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference/reference_markers.fasta -out GCF_000021985.1_ASM2198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,715] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:42,716] [INFO] Target genome list was writen to GCF_000021985.1_ASM2198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,725] [INFO] Task started: fastANI
[2024-01-24 13:28:42,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bff0cc5-7feb-4d4b-babb-7c13bd02fab0/GCF_000021985.1_ASM2198v1_genomic.fna.gz --refList GCF_000021985.1_ASM2198v1_genomic.fna/target_genomes.txt --output GCF_000021985.1_ASM2198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:53,750] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:53,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:53,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:53,762] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:53,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:53,763] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	100.0	1154	1154	95	conclusive
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	82.4397	629	1154	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	82.3551	646	1154	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	79.2258	345	1154	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	78.9393	293	1154	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	78.8419	362	1154	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	78.3838	343	1154	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	78.3334	274	1154	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	78.0101	285	1154	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	77.0714	308	1154	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.8595	166	1154	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.8028	216	1154	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.7147	223	1154	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.6072	115	1154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:53,764] [INFO] DFAST Taxonomy check result was written to GCF_000021985.1_ASM2198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:53,764] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:53,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:53,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference/checkm_data
[2024-01-24 13:28:53,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:53,800] [INFO] Task started: CheckM
[2024-01-24 13:28:53,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021985.1_ASM2198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021985.1_ASM2198v1_genomic.fna/checkm_input GCF_000021985.1_ASM2198v1_genomic.fna/checkm_result
[2024-01-24 13:29:32,515] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:32,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:32,532] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:32,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:32,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021985.1_ASM2198v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:32,534] [INFO] Task started: Blastn
[2024-01-24 13:29:32,534] [INFO] Running command: blastn -query GCF_000021985.1_ASM2198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87a6cd15-05c3-42da-a7fc-efd1935adf81/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021985.1_ASM2198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:34,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:34,635] [INFO] Selected 7 target genomes.
[2024-01-24 13:29:34,636] [INFO] Target genome list was writen to GCF_000021985.1_ASM2198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:34,641] [INFO] Task started: fastANI
[2024-01-24 13:29:34,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bff0cc5-7feb-4d4b-babb-7c13bd02fab0/GCF_000021985.1_ASM2198v1_genomic.fna.gz --refList GCF_000021985.1_ASM2198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021985.1_ASM2198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:41,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:41,141] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:41,141] [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_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	100.0	1154	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	94.61	852	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	82.4343	631	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	82.3556	646	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120155.1	s__Thioalkalivibrio_A sp007120155	81.9109	443	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	80.4107	418	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	79.9186	389	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,146] [INFO] GTDB search result was written to GCF_000021985.1_ASM2198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:41,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:41,150] [INFO] DFAST_QC result json was written to GCF_000021985.1_ASM2198v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:41,150] [INFO] DFAST_QC completed!
[2024-01-24 13:29:41,151] [INFO] Total running time: 0h1m12s