[2023-06-30 09:06:58,528] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:06:58,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:06:58,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference
[2023-06-30 09:06:59,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:06:59,735] [INFO] Task started: Prodigal
[2023-06-30 09:06:59,736] [INFO] Running command: gunzip -c /var/lib/cwl/stga6b80a32-3d00-40c8-97d9-db648f923075/GCA_024511925.1_ASM2451192v1_genomic.fna.gz | prodigal -d GCA_024511925.1_ASM2451192v1_genomic.fna/cds.fna -a GCA_024511925.1_ASM2451192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:07:05,814] [INFO] Task succeeded: Prodigal
[2023-06-30 09:07:05,814] [INFO] Task started: HMMsearch
[2023-06-30 09:07:05,815] [INFO] Running command: hmmsearch --tblout GCA_024511925.1_ASM2451192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference/reference_markers.hmm GCA_024511925.1_ASM2451192v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:07:06,060] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:07:06,062] [INFO] Found 6/6 markers.
[2023-06-30 09:07:06,089] [INFO] Query marker FASTA was written to GCA_024511925.1_ASM2451192v1_genomic.fna/markers.fasta
[2023-06-30 09:07:06,089] [INFO] Task started: Blastn
[2023-06-30 09:07:06,090] [INFO] Running command: blastn -query GCA_024511925.1_ASM2451192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference/reference_markers.fasta -out GCA_024511925.1_ASM2451192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:07:06,960] [INFO] Task succeeded: Blastn
[2023-06-30 09:07:06,981] [INFO] Selected 27 target genomes.
[2023-06-30 09:07:06,982] [INFO] Target genome list was writen to GCA_024511925.1_ASM2451192v1_genomic.fna/target_genomes.txt
[2023-06-30 09:07:06,983] [INFO] Task started: fastANI
[2023-06-30 09:07:06,983] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b80a32-3d00-40c8-97d9-db648f923075/GCA_024511925.1_ASM2451192v1_genomic.fna.gz --refList GCA_024511925.1_ASM2451192v1_genomic.fna/target_genomes.txt --output GCA_024511925.1_ASM2451192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:07:23,592] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:23,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:07:23,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:07:23,602] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:07:23,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:07:23,603] [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
Thiolapillus brandeum	strain=Hiromi 1	GCA_000828615.1	1076588	1076588	type	True	80.1423	344	617	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.1794	78	617	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.7934	62	617	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.64	74	617	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5978	85	617	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.5976	56	617	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.4757	58	617	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	76.3925	50	617	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.3886	66	617	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.3751	95	617	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.0571	66	617	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:07:23,605] [INFO] DFAST Taxonomy check result was written to GCA_024511925.1_ASM2451192v1_genomic.fna/tc_result.tsv
[2023-06-30 09:07:23,606] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:07:23,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:07:23,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference/checkm_data
[2023-06-30 09:07:23,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:07:23,640] [INFO] Task started: CheckM
[2023-06-30 09:07:23,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024511925.1_ASM2451192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024511925.1_ASM2451192v1_genomic.fna/checkm_input GCA_024511925.1_ASM2451192v1_genomic.fna/checkm_result
[2023-06-30 09:07:48,245] [INFO] Task succeeded: CheckM
[2023-06-30 09:07:48,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:07:48,273] [INFO] ===== Completeness check finished =====
[2023-06-30 09:07:48,273] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:07:48,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024511925.1_ASM2451192v1_genomic.fna/markers.fasta)
[2023-06-30 09:07:48,274] [INFO] Task started: Blastn
[2023-06-30 09:07:48,274] [INFO] Running command: blastn -query GCA_024511925.1_ASM2451192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1c5c618-8a68-445e-95fa-70f79392d24b/dqc_reference/reference_markers_gtdb.fasta -out GCA_024511925.1_ASM2451192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:07:49,824] [INFO] Task succeeded: Blastn
[2023-06-30 09:07:49,829] [INFO] Selected 14 target genomes.
[2023-06-30 09:07:49,829] [INFO] Target genome list was writen to GCA_024511925.1_ASM2451192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:07:49,829] [INFO] Task started: fastANI
[2023-06-30 09:07:49,830] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b80a32-3d00-40c8-97d9-db648f923075/GCA_024511925.1_ASM2451192v1_genomic.fna.gz --refList GCA_024511925.1_ASM2451192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024511925.1_ASM2451192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:07:57,414] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:57,431] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:07:57,431] [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_011051425.1	s__Thiolapillus brandeum_A	95.8929	410	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012962365.1	s__Thiolapillus sp012962365	80.9786	284	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828615.1	s__Thiolapillus brandeum	80.1469	345	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972985.1	s__Thiolapillus sp003972985	78.4576	251	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCF_000801295.1	s__MONJU sp000801295	77.1159	136	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	77.1092	73	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.9451	125	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	76.865	105	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	76.7942	79	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801995.1	s__YD12-FULL-61-37 sp001801995	76.7061	80	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__YD12-FULL-61-37	95.0	99.93	99.93	0.98	0.98	2	-
GCA_011389885.1	s__JABBTK01 sp011389885	76.3922	88	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JABBTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	75.8344	53	617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 09:07:57,433] [INFO] GTDB search result was written to GCA_024511925.1_ASM2451192v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:07:57,434] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:07:57,438] [INFO] DFAST_QC result json was written to GCA_024511925.1_ASM2451192v1_genomic.fna/dqc_result.json
[2023-06-30 09:07:57,438] [INFO] DFAST_QC completed!
[2023-06-30 09:07:57,438] [INFO] Total running time: 0h0m59s