[2023-06-28 20:26:40,073] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:26:40,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:26:40,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference
[2023-06-28 20:26:41,427] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:26:41,428] [INFO] Task started: Prodigal
[2023-06-28 20:26:41,429] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f9f7208-b2d7-4d0b-b92e-b1a89162d0c0/GCA_015492455.1_ASM1549245v1_genomic.fna.gz | prodigal -d GCA_015492455.1_ASM1549245v1_genomic.fna/cds.fna -a GCA_015492455.1_ASM1549245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:26:47,092] [INFO] Task succeeded: Prodigal
[2023-06-28 20:26:47,092] [INFO] Task started: HMMsearch
[2023-06-28 20:26:47,093] [INFO] Running command: hmmsearch --tblout GCA_015492455.1_ASM1549245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference/reference_markers.hmm GCA_015492455.1_ASM1549245v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:26:47,331] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:26:47,332] [INFO] Found 6/6 markers.
[2023-06-28 20:26:47,365] [INFO] Query marker FASTA was written to GCA_015492455.1_ASM1549245v1_genomic.fna/markers.fasta
[2023-06-28 20:26:47,366] [INFO] Task started: Blastn
[2023-06-28 20:26:47,366] [INFO] Running command: blastn -query GCA_015492455.1_ASM1549245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference/reference_markers.fasta -out GCA_015492455.1_ASM1549245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:26:48,259] [INFO] Task succeeded: Blastn
[2023-06-28 20:26:48,264] [INFO] Selected 31 target genomes.
[2023-06-28 20:26:48,264] [INFO] Target genome list was writen to GCA_015492455.1_ASM1549245v1_genomic.fna/target_genomes.txt
[2023-06-28 20:26:48,266] [INFO] Task started: fastANI
[2023-06-28 20:26:48,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f9f7208-b2d7-4d0b-b92e-b1a89162d0c0/GCA_015492455.1_ASM1549245v1_genomic.fna.gz --refList GCA_015492455.1_ASM1549245v1_genomic.fna/target_genomes.txt --output GCA_015492455.1_ASM1549245v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:27:07,876] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:07,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:27:07,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:27:07,895] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:27:07,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:27:07,895] [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
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.532	145	570	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	77.4871	106	570	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.4596	132	570	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.3802	114	570	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	77.0425	96	570	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.9414	104	570	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.9141	124	570	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8594	114	570	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.7007	82	570	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.5295	57	570	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	76.4101	62	570	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.3544	68	570	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.3374	76	570	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.327	77	570	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	76.2839	61	570	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.2738	60	570	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.2093	56	570	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	76.2002	60	570	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	76.1595	53	570	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	76.1285	63	570	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	76.1256	51	570	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.7985	77	570	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:27:07,898] [INFO] DFAST Taxonomy check result was written to GCA_015492455.1_ASM1549245v1_genomic.fna/tc_result.tsv
[2023-06-28 20:27:07,899] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:27:07,899] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:27:07,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference/checkm_data
[2023-06-28 20:27:07,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:27:07,933] [INFO] Task started: CheckM
[2023-06-28 20:27:07,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015492455.1_ASM1549245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015492455.1_ASM1549245v1_genomic.fna/checkm_input GCA_015492455.1_ASM1549245v1_genomic.fna/checkm_result
[2023-06-28 20:27:30,493] [INFO] Task succeeded: CheckM
[2023-06-28 20:27:30,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 20:27:30,529] [INFO] ===== Completeness check finished =====
[2023-06-28 20:27:30,529] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:27:30,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015492455.1_ASM1549245v1_genomic.fna/markers.fasta)
[2023-06-28 20:27:30,530] [INFO] Task started: Blastn
[2023-06-28 20:27:30,530] [INFO] Running command: blastn -query GCA_015492455.1_ASM1549245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb2e6991-f200-423e-afc3-160ce5daea4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_015492455.1_ASM1549245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:27:31,852] [INFO] Task succeeded: Blastn
[2023-06-28 20:27:31,856] [INFO] Selected 14 target genomes.
[2023-06-28 20:27:31,856] [INFO] Target genome list was writen to GCA_015492455.1_ASM1549245v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:27:31,857] [INFO] Task started: fastANI
[2023-06-28 20:27:31,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f9f7208-b2d7-4d0b-b92e-b1a89162d0c0/GCA_015492455.1_ASM1549245v1_genomic.fna.gz --refList GCA_015492455.1_ASM1549245v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015492455.1_ASM1549245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:27:40,365] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:40,383] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:27:40,384] [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_015490535.1	s__DRMK01 sp015490535	99.2299	501	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	99.14	99.14	0.88	0.88	2	conclusive
GCA_011322575.1	s__DRMK01 sp011322575	91.0323	289	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491735.1	s__DRMK01 sp015491735	80.7218	186	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	99.89	99.89	0.95	0.95	2	-
GCA_015488495.1	s__DRMK01 sp015488495	79.7008	271	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRMK01;f__DRMK01;g__DRMK01	95.0	98.86	98.62	0.82	0.79	5	-
GCA_011051715.1	s__HyVt-443 sp011051715	77.553	128	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	77.5109	146	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.4596	132	570	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_011371455.1	s__DRQN01 sp011371455	77.4587	89	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_003751635.1	s__Inmirania thermothiophila	77.4041	113	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.0903	131	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_000377845.1	s__Thioalkalivibrio sp000377845	76.3465	53	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	75.8209	55	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:27:40,386] [INFO] GTDB search result was written to GCA_015492455.1_ASM1549245v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:27:40,387] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:27:40,392] [INFO] DFAST_QC result json was written to GCA_015492455.1_ASM1549245v1_genomic.fna/dqc_result.json
[2023-06-28 20:27:40,392] [INFO] DFAST_QC completed!
[2023-06-28 20:27:40,393] [INFO] Total running time: 0h1m0s