[2024-01-24 12:09:05,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference
[2024-01-24 12:09:07,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:07,001] [INFO] Task started: Prodigal
[2024-01-24 12:09:07,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg46c62b74-a8f1-415d-9610-647f07692a93/GCF_002355735.1_ASM235573v1_genomic.fna.gz | prodigal -d GCF_002355735.1_ASM235573v1_genomic.fna/cds.fna -a GCF_002355735.1_ASM235573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:15,894] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:15,894] [INFO] Task started: HMMsearch
[2024-01-24 12:09:15,895] [INFO] Running command: hmmsearch --tblout GCF_002355735.1_ASM235573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference/reference_markers.hmm GCF_002355735.1_ASM235573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:16,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:16,147] [INFO] Found 6/6 markers.
[2024-01-24 12:09:16,183] [INFO] Query marker FASTA was written to GCF_002355735.1_ASM235573v1_genomic.fna/markers.fasta
[2024-01-24 12:09:16,183] [INFO] Task started: Blastn
[2024-01-24 12:09:16,183] [INFO] Running command: blastn -query GCF_002355735.1_ASM235573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference/reference_markers.fasta -out GCF_002355735.1_ASM235573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:17,156] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:17,159] [INFO] Selected 25 target genomes.
[2024-01-24 12:09:17,159] [INFO] Target genome list was writen to GCF_002355735.1_ASM235573v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:17,168] [INFO] Task started: fastANI
[2024-01-24 12:09:17,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c62b74-a8f1-415d-9610-647f07692a93/GCF_002355735.1_ASM235573v1_genomic.fna.gz --refList GCF_002355735.1_ASM235573v1_genomic.fna/target_genomes.txt --output GCF_002355735.1_ASM235573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:33,049] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:33,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:33,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:33,071] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:33,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:33,072] [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
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	100.0	954	954	95	conclusive
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	78.1416	287	954	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.302	156	954	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.2445	190	954	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.1047	184	954	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	77.0579	78	954	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.9588	63	954	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.9383	117	954	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.8073	100	954	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.703	132	954	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	76.6953	98	954	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6586	146	954	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.6448	118	954	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	76.6412	100	954	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.6138	100	954	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.6075	123	954	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.5229	197	954	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	76.4384	103	954	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3792	154	954	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	76.3511	100	954	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	76.2902	165	954	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.2676	161	954	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.1836	161	954	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	75.7471	70	954	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:33,073] [INFO] DFAST Taxonomy check result was written to GCF_002355735.1_ASM235573v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:33,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:33,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:33,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference/checkm_data
[2024-01-24 12:09:33,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:33,109] [INFO] Task started: CheckM
[2024-01-24 12:09:33,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355735.1_ASM235573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355735.1_ASM235573v1_genomic.fna/checkm_input GCF_002355735.1_ASM235573v1_genomic.fna/checkm_result
[2024-01-24 12:10:03,246] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:03,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:03,266] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:03,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:03,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355735.1_ASM235573v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:03,267] [INFO] Task started: Blastn
[2024-01-24 12:10:03,267] [INFO] Running command: blastn -query GCF_002355735.1_ASM235573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4406032b-5cdd-4b4c-8157-e009f4f80682/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355735.1_ASM235573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:05,128] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:05,131] [INFO] Selected 10 target genomes.
[2024-01-24 12:10:05,132] [INFO] Target genome list was writen to GCF_002355735.1_ASM235573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:05,139] [INFO] Task started: fastANI
[2024-01-24 12:10:05,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c62b74-a8f1-415d-9610-647f07692a93/GCF_002355735.1_ASM235573v1_genomic.fna.gz --refList GCF_002355735.1_ASM235573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355735.1_ASM235573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:11,047] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:11,057] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:11,057] [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_002355735.1	s__Sulfuricaulis limicola	100.0	954	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001785195.1	s__Sulfuricaulis sp001785195	84.9493	455	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	99.70	99.65	0.87	0.80	5	-
GCA_016200465.1	s__Sulfuricaulis sp016200465	82.8806	427	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001785175.1	s__MFSY01 sp001785175	79.7151	285	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__MFSY01	95.0	97.98	97.98	0.76	0.76	2	-
GCA_004298065.1	s__SCRL01 sp004298065	79.6778	382	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__SCRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355415.1	s__Sulfurifustis variabilis	78.1294	288	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfurifustis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016194665.1	s__Sulfuricaulis sp016194665	77.9575	235	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199745.1	s__JACQFZ01 sp016199745	76.8178	167	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__JACQFZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595175.1	s__Pseudomonas_E sp003595175	76.5076	123	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179555.1	s__Salinicola salarius_A	76.2266	63	954	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:11,059] [INFO] GTDB search result was written to GCF_002355735.1_ASM235573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:11,059] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:11,063] [INFO] DFAST_QC result json was written to GCF_002355735.1_ASM235573v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:11,063] [INFO] DFAST_QC completed!
[2024-01-24 12:10:11,063] [INFO] Total running time: 0h1m5s