[2023-06-19 08:13:04,483] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:13:04,485] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:13:04,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference
[2023-06-19 08:13:05,924] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:13:05,929] [INFO] Task started: Prodigal
[2023-06-19 08:13:05,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb7dedbe-6454-42b8-b437-27bf4d5f1dfb/GCA_018671485.1_ASM1867148v1_genomic.fna.gz | prodigal -d GCA_018671485.1_ASM1867148v1_genomic.fna/cds.fna -a GCA_018671485.1_ASM1867148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:13:08,088] [INFO] Task succeeded: Prodigal
[2023-06-19 08:13:08,089] [INFO] Task started: HMMsearch
[2023-06-19 08:13:08,089] [INFO] Running command: hmmsearch --tblout GCA_018671485.1_ASM1867148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference/reference_markers.hmm GCA_018671485.1_ASM1867148v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:13:08,301] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:13:08,302] [INFO] Found 6/6 markers.
[2023-06-19 08:13:08,317] [INFO] Query marker FASTA was written to GCA_018671485.1_ASM1867148v1_genomic.fna/markers.fasta
[2023-06-19 08:13:08,318] [INFO] Task started: Blastn
[2023-06-19 08:13:08,318] [INFO] Running command: blastn -query GCA_018671485.1_ASM1867148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference/reference_markers.fasta -out GCA_018671485.1_ASM1867148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:13:08,904] [INFO] Task succeeded: Blastn
[2023-06-19 08:13:08,908] [INFO] Selected 31 target genomes.
[2023-06-19 08:13:08,908] [INFO] Target genome list was writen to GCA_018671485.1_ASM1867148v1_genomic.fna/target_genomes.txt
[2023-06-19 08:13:08,912] [INFO] Task started: fastANI
[2023-06-19 08:13:08,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb7dedbe-6454-42b8-b437-27bf4d5f1dfb/GCA_018671485.1_ASM1867148v1_genomic.fna.gz --refList GCA_018671485.1_ASM1867148v1_genomic.fna/target_genomes.txt --output GCA_018671485.1_ASM1867148v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:13:27,142] [INFO] Task succeeded: fastANI
[2023-06-19 08:13:27,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:13:27,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:13:27,148] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:13:27,148] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:13:27,148] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	78.1601	105	257	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:13:27,150] [INFO] DFAST Taxonomy check result was written to GCA_018671485.1_ASM1867148v1_genomic.fna/tc_result.tsv
[2023-06-19 08:13:27,151] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:13:27,151] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:13:27,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference/checkm_data
[2023-06-19 08:13:27,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:13:27,168] [INFO] Task started: CheckM
[2023-06-19 08:13:27,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018671485.1_ASM1867148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018671485.1_ASM1867148v1_genomic.fna/checkm_input GCA_018671485.1_ASM1867148v1_genomic.fna/checkm_result
[2023-06-19 08:13:43,603] [INFO] Task succeeded: CheckM
[2023-06-19 08:13:43,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 11.74%
Strain heterogeneity: 90.91%
--------------------------------------------------------------------------------
[2023-06-19 08:13:43,626] [INFO] ===== Completeness check finished =====
[2023-06-19 08:13:43,627] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:13:43,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018671485.1_ASM1867148v1_genomic.fna/markers.fasta)
[2023-06-19 08:13:43,627] [INFO] Task started: Blastn
[2023-06-19 08:13:43,627] [INFO] Running command: blastn -query GCA_018671485.1_ASM1867148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e374062-db11-4442-ac5a-cd765ed8a399/dqc_reference/reference_markers_gtdb.fasta -out GCA_018671485.1_ASM1867148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:13:44,457] [INFO] Task succeeded: Blastn
[2023-06-19 08:13:44,462] [INFO] Selected 17 target genomes.
[2023-06-19 08:13:44,462] [INFO] Target genome list was writen to GCA_018671485.1_ASM1867148v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:13:44,468] [INFO] Task started: fastANI
[2023-06-19 08:13:44,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb7dedbe-6454-42b8-b437-27bf4d5f1dfb/GCA_018671485.1_ASM1867148v1_genomic.fna.gz --refList GCA_018671485.1_ASM1867148v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018671485.1_ASM1867148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:13:49,218] [INFO] Task succeeded: fastANI
[2023-06-19 08:13:49,231] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:13:49,231] [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
GCA_000205985.2	s__SUP05 sp000205985	99.2988	209	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__SUP05	95.0	99.29	99.11	0.83	0.80	14	conclusive
GCA_018648985.1	s__UBA2013 sp018648985	79.9426	126	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003489145.1	s__UBA2013 sp003489145	79.6808	119	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_016845205.1	s__UBA2013 sp016845205	79.3787	136	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978285.1	s__UBA2013 sp003978285	79.0291	91	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335045.1	s__UBA2013 sp002335045	78.981	136	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_003978185.1	s__UBA2013 sp003978185	78.4932	78	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293165.1	s__Thioglobus autotrophicus	78.1601	105	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900180385.1	s__Thioglobus sp900180385	77.9964	105	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018644675.1	s__Thioglobus sp018644675	77.9901	101	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.74	99.56	0.96	0.91	16	-
GCA_012963565.1	s__DTVJ01 sp012963565	77.9689	103	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592615.1	s__Ruthia sp016592615	77.8914	90	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Ruthia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128535.1	s__Thiodubiliella sp900128535	77.4839	74	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.14	96.23	0.87	0.79	15	-
GCA_014384345.1	s__Thioglobus pontius	77.4729	105	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCF_001298715.1	s__Thiodubiliella sp001298715	77.4096	65	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.96	97.97	0.90	0.82	38	-
--------------------------------------------------------------------------------
[2023-06-19 08:13:49,236] [INFO] GTDB search result was written to GCA_018671485.1_ASM1867148v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:13:49,237] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:13:49,240] [INFO] DFAST_QC result json was written to GCA_018671485.1_ASM1867148v1_genomic.fna/dqc_result.json
[2023-06-19 08:13:49,240] [INFO] DFAST_QC completed!
[2023-06-19 08:13:49,240] [INFO] Total running time: 0h0m45s