[2024-01-24 11:05:34,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference
[2024-01-24 11:05:35,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,909] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgc19db589-c17e-4bab-b5e1-4ef363c7b19c/GCF_002000365.1_ASM200036v1_genomic.fna.gz | prodigal -d GCF_002000365.1_ASM200036v1_genomic.fna/cds.fna -a GCF_002000365.1_ASM200036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:46,800] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:46,801] [INFO] Task started: HMMsearch
[2024-01-24 11:05:46,801] [INFO] Running command: hmmsearch --tblout GCF_002000365.1_ASM200036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference/reference_markers.hmm GCF_002000365.1_ASM200036v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:47,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:47,108] [INFO] Found 6/6 markers.
[2024-01-24 11:05:47,140] [INFO] Query marker FASTA was written to GCF_002000365.1_ASM200036v1_genomic.fna/markers.fasta
[2024-01-24 11:05:47,141] [INFO] Task started: Blastn
[2024-01-24 11:05:47,141] [INFO] Running command: blastn -query GCF_002000365.1_ASM200036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference/reference_markers.fasta -out GCF_002000365.1_ASM200036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:48,092] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:48,096] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:48,097] [INFO] Target genome list was writen to GCF_002000365.1_ASM200036v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:48,107] [INFO] Task started: fastANI
[2024-01-24 11:05:48,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgc19db589-c17e-4bab-b5e1-4ef363c7b19c/GCF_002000365.1_ASM200036v1_genomic.fna.gz --refList GCF_002000365.1_ASM200036v1_genomic.fna/target_genomes.txt --output GCF_002000365.1_ASM200036v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:59,614] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:59,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:59,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:59,631] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:59,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:59,631] [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 denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	100.0	1116	1123	95	conclusive
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	82.3426	648	1123	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	82.2334	666	1123	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	78.1921	221	1123	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	78.0192	206	1123	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	77.9597	273	1123	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	77.8907	210	1123	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.6387	252	1123	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	76.9938	171	1123	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.8972	121	1123	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.8534	148	1123	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.8257	144	1123	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	76.6562	128	1123	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.6091	106	1123	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	76.1629	99	1123	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.0021	105	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:59,633] [INFO] DFAST Taxonomy check result was written to GCF_002000365.1_ASM200036v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:59,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:59,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:59,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference/checkm_data
[2024-01-24 11:05:59,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:59,675] [INFO] Task started: CheckM
[2024-01-24 11:05:59,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000365.1_ASM200036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000365.1_ASM200036v1_genomic.fna/checkm_input GCF_002000365.1_ASM200036v1_genomic.fna/checkm_result
[2024-01-24 11:06:37,187] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:37,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,209] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:37,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:37,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000365.1_ASM200036v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:37,210] [INFO] Task started: Blastn
[2024-01-24 11:06:37,211] [INFO] Running command: blastn -query GCF_002000365.1_ASM200036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d8c3da-2920-45cc-8604-4e343d839a59/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000365.1_ASM200036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:38,976] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:38,980] [INFO] Selected 8 target genomes.
[2024-01-24 11:06:38,980] [INFO] Target genome list was writen to GCF_002000365.1_ASM200036v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:38,990] [INFO] Task started: fastANI
[2024-01-24 11:06:38,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgc19db589-c17e-4bab-b5e1-4ef363c7b19c/GCF_002000365.1_ASM200036v1_genomic.fna.gz --refList GCF_002000365.1_ASM200036v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000365.1_ASM200036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:45,922] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:45,938] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:45,938] [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_002000365.1	s__Thioalkalivibrio_A denitrificans	100.0	1116	1123	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	82.4016	625	1123	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_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	82.3801	645	1123	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	82.2932	660	1123	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	81.909	479	1123	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	79.0768	319	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	78.5861	311	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	78.4814	294	1123	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 11:06:45,940] [INFO] GTDB search result was written to GCF_002000365.1_ASM200036v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:45,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:45,944] [INFO] DFAST_QC result json was written to GCF_002000365.1_ASM200036v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:45,944] [INFO] DFAST_QC completed!
[2024-01-24 11:06:45,944] [INFO] Total running time: 0h1m11s