[2024-01-25 18:42:05,638] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference
[2024-01-25 18:42:06,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,780] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg5172dad3-cc2b-4710-9b64-88b6086cd8a7/GCF_000321415.2_ASM32141v2_genomic.fna.gz | prodigal -d GCF_000321415.2_ASM32141v2_genomic.fna/cds.fna -a GCF_000321415.2_ASM32141v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:17,456] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:17,456] [INFO] Task started: HMMsearch
[2024-01-25 18:42:17,456] [INFO] Running command: hmmsearch --tblout GCF_000321415.2_ASM32141v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference/reference_markers.hmm GCF_000321415.2_ASM32141v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:17,678] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:17,679] [INFO] Found 6/6 markers.
[2024-01-25 18:42:17,709] [INFO] Query marker FASTA was written to GCF_000321415.2_ASM32141v2_genomic.fna/markers.fasta
[2024-01-25 18:42:17,710] [INFO] Task started: Blastn
[2024-01-25 18:42:17,710] [INFO] Running command: blastn -query GCF_000321415.2_ASM32141v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference/reference_markers.fasta -out GCF_000321415.2_ASM32141v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:18,594] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:18,599] [INFO] Selected 14 target genomes.
[2024-01-25 18:42:18,599] [INFO] Target genome list was writen to GCF_000321415.2_ASM32141v2_genomic.fna/target_genomes.txt
[2024-01-25 18:42:18,603] [INFO] Task started: fastANI
[2024-01-25 18:42:18,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg5172dad3-cc2b-4710-9b64-88b6086cd8a7/GCF_000321415.2_ASM32141v2_genomic.fna.gz --refList GCF_000321415.2_ASM32141v2_genomic.fna/target_genomes.txt --output GCF_000321415.2_ASM32141v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:29,092] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:29,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:29,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:29,101] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:29,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:29,101] [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 nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	100.0	1332	1334	95	conclusive
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	89.657	1022	1334	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	78.7751	312	1334	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	78.4916	303	1334	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	78.3436	319	1334	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	77.0505	107	1334	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	76.9244	129	1334	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.8856	129	1334	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5339	143	1334	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	76.4683	96	1334	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3244	114	1334	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.0561	114	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:29,102] [INFO] DFAST Taxonomy check result was written to GCF_000321415.2_ASM32141v2_genomic.fna/tc_result.tsv
[2024-01-25 18:42:29,103] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:29,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:29,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference/checkm_data
[2024-01-25 18:42:29,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:29,144] [INFO] Task started: CheckM
[2024-01-25 18:42:29,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000321415.2_ASM32141v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000321415.2_ASM32141v2_genomic.fna/checkm_input GCF_000321415.2_ASM32141v2_genomic.fna/checkm_result
[2024-01-25 18:43:11,819] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:11,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:11,853] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:11,854] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:11,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000321415.2_ASM32141v2_genomic.fna/markers.fasta)
[2024-01-25 18:43:11,854] [INFO] Task started: Blastn
[2024-01-25 18:43:11,854] [INFO] Running command: blastn -query GCF_000321415.2_ASM32141v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c91f626-d05a-44ac-9da0-e02c6b78e04a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000321415.2_ASM32141v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:13,606] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:13,609] [INFO] Selected 14 target genomes.
[2024-01-25 18:43:13,609] [INFO] Target genome list was writen to GCF_000321415.2_ASM32141v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:13,619] [INFO] Task started: fastANI
[2024-01-25 18:43:13,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg5172dad3-cc2b-4710-9b64-88b6086cd8a7/GCF_000321415.2_ASM32141v2_genomic.fna.gz --refList GCF_000321415.2_ASM32141v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000321415.2_ASM32141v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:24,216] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:24,225] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:24,225] [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_000321415.2	s__Thioalkalivibrio_B nitratireducens	100.0	1332	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000227685.2	s__Thioalkalivibrio_B paradoxus	89.6606	1021	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007116035.1	s__Thioalkalivibrio_B sp007116035	80.2873	502	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	99.33	99.33	0.75	0.75	2	-
GCA_003550945.1	s__Thioalkalivibrio_B sp003550945	80.2388	306	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692435.1	s__Thioalkalivibrio_B sp007692435	80.0906	454	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692535.1	s__Thioalkalivibrio_B sp007692535	80.0474	511	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389655.1	s__Thioalkalivibrio_B sp011389655	79.976	453	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003555285.1	s__Thioalkalivibrio_B sp003555285	79.7459	399	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390565.1	s__Thioalkalivibrio_B paradoxus_A	79.7362	438	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003563455.1	s__Thioalkalivibrio_B sp003563455	79.6573	327	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	98.96	98.96	0.85	0.85	2	-
GCA_007133115.1	s__Thioalkalivibrio_B sp007133115	79.4176	212	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	78.5038	302	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_012272825.1	s__GCA-2722315 sp012272825	76.7326	136	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733765.1	s__Algiphilus aromaticivorans	76.4683	96	1334	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Algiphilaceae;g__Algiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:24,228] [INFO] GTDB search result was written to GCF_000321415.2_ASM32141v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:24,230] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:24,233] [INFO] DFAST_QC result json was written to GCF_000321415.2_ASM32141v2_genomic.fna/dqc_result.json
[2024-01-25 18:43:24,233] [INFO] DFAST_QC completed!
[2024-01-25 18:43:24,233] [INFO] Total running time: 0h1m19s