[2023-06-13 20:23:47,772] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:23:47,776] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:23:47,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference
[2023-06-13 20:23:49,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:23:49,365] [INFO] Task started: Prodigal
[2023-06-13 20:23:49,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2839746-1f98-45a9-ac8f-43cf85ab480b/GCA_022841785.1_ASM2284178v1_genomic.fna.gz | prodigal -d GCA_022841785.1_ASM2284178v1_genomic.fna/cds.fna -a GCA_022841785.1_ASM2284178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:23:59,119] [INFO] Task succeeded: Prodigal
[2023-06-13 20:23:59,120] [INFO] Task started: HMMsearch
[2023-06-13 20:23:59,120] [INFO] Running command: hmmsearch --tblout GCA_022841785.1_ASM2284178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference/reference_markers.hmm GCA_022841785.1_ASM2284178v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:23:59,382] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:23:59,383] [INFO] Found 6/6 markers.
[2023-06-13 20:23:59,422] [INFO] Query marker FASTA was written to GCA_022841785.1_ASM2284178v1_genomic.fna/markers.fasta
[2023-06-13 20:23:59,422] [INFO] Task started: Blastn
[2023-06-13 20:23:59,422] [INFO] Running command: blastn -query GCA_022841785.1_ASM2284178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference/reference_markers.fasta -out GCA_022841785.1_ASM2284178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:00,262] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:00,266] [INFO] Selected 23 target genomes.
[2023-06-13 20:24:00,266] [INFO] Target genome list was writen to GCA_022841785.1_ASM2284178v1_genomic.fna/target_genomes.txt
[2023-06-13 20:24:00,269] [INFO] Task started: fastANI
[2023-06-13 20:24:00,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2839746-1f98-45a9-ac8f-43cf85ab480b/GCA_022841785.1_ASM2284178v1_genomic.fna.gz --refList GCA_022841785.1_ASM2284178v1_genomic.fna/target_genomes.txt --output GCA_022841785.1_ASM2284178v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:24:16,956] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:16,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:24:16,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:24:16,970] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:24:16,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:24:16,970] [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
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.7934	251	1167	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.6982	268	1167	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.5059	245	1167	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	77.3847	201	1167	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	77.326	179	1167	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	77.3044	183	1167	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	77.1071	193	1167	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.8305	127	1167	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.8272	132	1167	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	76.5214	98	1167	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	76.4495	138	1167	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	76.3696	97	1167	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.3564	150	1167	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.3095	115	1167	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.2729	99	1167	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	76.2191	82	1167	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.1586	142	1167	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	76.1509	110	1167	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	76.1441	109	1167	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.8781	135	1167	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.8202	72	1167	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	75.8109	60	1167	95	below_threshold
Rhodoligotrophos appendicifer	strain=120-1	GCA_007474605.1	987056	987056	type	True	75.6355	60	1167	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:24:16,972] [INFO] DFAST Taxonomy check result was written to GCA_022841785.1_ASM2284178v1_genomic.fna/tc_result.tsv
[2023-06-13 20:24:16,972] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:24:16,973] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:24:16,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference/checkm_data
[2023-06-13 20:24:16,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:24:17,011] [INFO] Task started: CheckM
[2023-06-13 20:24:17,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022841785.1_ASM2284178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022841785.1_ASM2284178v1_genomic.fna/checkm_input GCA_022841785.1_ASM2284178v1_genomic.fna/checkm_result
[2023-06-13 20:24:47,256] [INFO] Task succeeded: CheckM
[2023-06-13 20:24:47,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:24:47,276] [INFO] ===== Completeness check finished =====
[2023-06-13 20:24:47,276] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:24:47,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022841785.1_ASM2284178v1_genomic.fna/markers.fasta)
[2023-06-13 20:24:47,277] [INFO] Task started: Blastn
[2023-06-13 20:24:47,278] [INFO] Running command: blastn -query GCA_022841785.1_ASM2284178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e0e00a2-f7c1-491e-8f34-0112f5d976cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022841785.1_ASM2284178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:48,834] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:48,838] [INFO] Selected 14 target genomes.
[2023-06-13 20:24:48,838] [INFO] Target genome list was writen to GCA_022841785.1_ASM2284178v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:24:48,845] [INFO] Task started: fastANI
[2023-06-13 20:24:48,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2839746-1f98-45a9-ac8f-43cf85ab480b/GCA_022841785.1_ASM2284178v1_genomic.fna.gz --refList GCA_022841785.1_ASM2284178v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022841785.1_ASM2284178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:24:58,927] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:58,936] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:24:58,937] [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_002928735.1	s__Hyphomicrobium sp002928735	98.8959	996	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.98	99.98	0.93	0.93	2	conclusive
GCA_002279935.1	s__Hyphomicrobium sp002279935	91.7062	983	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.98	99.98	0.99	0.99	2	-
GCA_001464285.1	s__Hyphomicrobium sp001464285	79.5316	533	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	77.6982	268	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	77.6473	209	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	77.5264	194	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019137195.1	s__Hyphomicrobium sp019137195	77.4641	240	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	77.4052	248	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	77.3656	245	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013306565.1	s__Hyphomicrobium_A sulfonivorans	77.3044	183	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	98.55	97.10	0.95	0.91	3	-
GCA_013141015.1	s__Hyphomicrobium sp013141015	77.2466	195	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	76.5121	138	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900079695.1	s__Alpha-05 sp900079695	75.911	73	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679265.1	s__MT2928 sp015679265	75.8393	71	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:24:58,938] [INFO] GTDB search result was written to GCA_022841785.1_ASM2284178v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:24:58,939] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:24:58,942] [INFO] DFAST_QC result json was written to GCA_022841785.1_ASM2284178v1_genomic.fna/dqc_result.json
[2023-06-13 20:24:58,942] [INFO] DFAST_QC completed!
[2023-06-13 20:24:58,942] [INFO] Total running time: 0h1m11s