[2024-01-24 11:20:34,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference
[2024-01-24 11:20:35,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,683] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fd6fec2-ea99-4235-9c19-5de894904ac4/GCF_025567085.1_ASM2556708v1_genomic.fna.gz | prodigal -d GCF_025567085.1_ASM2556708v1_genomic.fna/cds.fna -a GCF_025567085.1_ASM2556708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:41,339] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:41,340] [INFO] Task started: HMMsearch
[2024-01-24 11:20:41,340] [INFO] Running command: hmmsearch --tblout GCF_025567085.1_ASM2556708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference/reference_markers.hmm GCF_025567085.1_ASM2556708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:41,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:41,584] [INFO] Found 6/6 markers.
[2024-01-24 11:20:41,609] [INFO] Query marker FASTA was written to GCF_025567085.1_ASM2556708v1_genomic.fna/markers.fasta
[2024-01-24 11:20:41,609] [INFO] Task started: Blastn
[2024-01-24 11:20:41,609] [INFO] Running command: blastn -query GCF_025567085.1_ASM2556708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference/reference_markers.fasta -out GCF_025567085.1_ASM2556708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:42,190] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:42,194] [INFO] Selected 31 target genomes.
[2024-01-24 11:20:42,194] [INFO] Target genome list was writen to GCF_025567085.1_ASM2556708v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:42,334] [INFO] Task started: fastANI
[2024-01-24 11:20:42,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd6fec2-ea99-4235-9c19-5de894904ac4/GCF_025567085.1_ASM2556708v1_genomic.fna.gz --refList GCF_025567085.1_ASM2556708v1_genomic.fna/target_genomes.txt --output GCF_025567085.1_ASM2556708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:56,639] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:56,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:56,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:56,663] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:56,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:56,663] [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
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	85.7134	112	997	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	84.3131	70	997	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	83.658	66	997	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	81.4691	50	997	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.7103	58	997	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	80.3257	102	997	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	80.2673	58	997	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	80.0965	123	997	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.0168	73	997	95	below_threshold
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	78.5852	70	997	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	77.6901	59	997	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	77.4604	69	997	95	below_threshold
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	77.0768	65	997	95	below_threshold
Lachnoclostridium phytofermentans	strain=ISDg	GCA_000018685.1	66219	66219	type	True	76.9175	60	997	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	76.7291	62	997	95	below_threshold
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	76.6377	67	997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,665] [INFO] DFAST Taxonomy check result was written to GCF_025567085.1_ASM2556708v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:56,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:56,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:56,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference/checkm_data
[2024-01-24 11:20:56,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:56,699] [INFO] Task started: CheckM
[2024-01-24 11:20:56,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567085.1_ASM2556708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567085.1_ASM2556708v1_genomic.fna/checkm_input GCF_025567085.1_ASM2556708v1_genomic.fna/checkm_result
[2024-01-24 11:21:20,108] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:20,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:20,128] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:20,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:20,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567085.1_ASM2556708v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:20,129] [INFO] Task started: Blastn
[2024-01-24 11:21:20,129] [INFO] Running command: blastn -query GCF_025567085.1_ASM2556708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a86bfeb-b08d-4336-bbed-f0fe7b37475e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567085.1_ASM2556708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:20,922] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:20,925] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:20,925] [INFO] Target genome list was writen to GCF_025567085.1_ASM2556708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:20,962] [INFO] Task started: fastANI
[2024-01-24 11:21:20,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd6fec2-ea99-4235-9c19-5de894904ac4/GCF_025567085.1_ASM2556708v1_genomic.fna.gz --refList GCF_025567085.1_ASM2556708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567085.1_ASM2556708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:28,097] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:28,110] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:28,110] [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_902362455.1	s__CAG-603 sp900066105	100.0	997	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.95	98.18	0.94	0.88	5	conclusive
GCA_900314555.1	s__CAG-603 sp900314555	94.0401	703	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900314525.1	s__CAG-603 sp900314525	78.8344	172	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.63	99.55	0.90	0.85	5	-
GCA_017416465.1	s__CAG-603 sp017416465	78.756	226	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539455.1	s__CAG-303 sp900539455	78.4639	114	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	99.77	99.53	0.98	0.96	3	-
GCA_902786365.1	s__CAG-603 sp902786365	78.3061	201	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002351535.1	s__UBA2821 sp002351535	78.2146	154	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCA_900110975.1	s__CAG-603 sp900110975	78.1066	155	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.39	98.39	0.96	0.96	2	-
GCA_900321855.1	s__CAG-603 sp900321855	77.706	112	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.42	99.42	0.95	0.95	2	-
GCA_900184995.1	s__Lachnotalea sp900184995	77.6901	59	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017424235.1	s__COE1 sp017424235	77.3687	75	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.29	98.29	0.84	0.84	2	-
GCA_017408025.1	s__CAG-303 sp017408025	76.9366	78	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:28,112] [INFO] GTDB search result was written to GCF_025567085.1_ASM2556708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:28,112] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:28,115] [INFO] DFAST_QC result json was written to GCF_025567085.1_ASM2556708v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:28,115] [INFO] DFAST_QC completed!
[2024-01-24 11:21:28,116] [INFO] Total running time: 0h0m54s