[2024-01-25 20:15:35,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:35,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:35,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference
[2024-01-25 20:15:36,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:36,683] [INFO] Task started: Prodigal
[2024-01-25 20:15:36,683] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2dff3e3-8546-4ae6-b0ef-2fdee55dcd79/GCF_000741775.1_Bifsub_genomic.fna.gz | prodigal -d GCF_000741775.1_Bifsub_genomic.fna/cds.fna -a GCF_000741775.1_Bifsub_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:44,566] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:44,566] [INFO] Task started: HMMsearch
[2024-01-25 20:15:44,566] [INFO] Running command: hmmsearch --tblout GCF_000741775.1_Bifsub_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference/reference_markers.hmm GCF_000741775.1_Bifsub_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:44,765] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:44,766] [INFO] Found 6/6 markers.
[2024-01-25 20:15:44,787] [INFO] Query marker FASTA was written to GCF_000741775.1_Bifsub_genomic.fna/markers.fasta
[2024-01-25 20:15:44,787] [INFO] Task started: Blastn
[2024-01-25 20:15:44,787] [INFO] Running command: blastn -query GCF_000741775.1_Bifsub_genomic.fna/markers.fasta -db /var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference/reference_markers.fasta -out GCF_000741775.1_Bifsub_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:45,696] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:45,698] [INFO] Selected 15 target genomes.
[2024-01-25 20:15:45,698] [INFO] Target genome list was writen to GCF_000741775.1_Bifsub_genomic.fna/target_genomes.txt
[2024-01-25 20:15:45,703] [INFO] Task started: fastANI
[2024-01-25 20:15:45,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2dff3e3-8546-4ae6-b0ef-2fdee55dcd79/GCF_000741775.1_Bifsub_genomic.fna.gz --refList GCF_000741775.1_Bifsub_genomic.fna/target_genomes.txt --output GCF_000741775.1_Bifsub_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:54,875] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:54,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:54,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:54,886] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:15:54,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:54,886] [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
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	100.0	915	916	95	conclusive
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	99.9682	882	916	95	conclusive
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	99.9583	899	916	95	conclusive
Bifidobacterium tibiigranuli	strain=TMW 2.2057	GCA_009371885.1	2172043	2172043	type	True	89.4504	680	916	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.9521	341	916	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	79.8274	320	916	95	below_threshold
Bifidobacterium mongoliense	strain=DSM 21395	GCA_000771525.1	518643	518643	type	True	79.7057	292	916	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.593	327	916	95	below_threshold
Bifidobacterium pullorum subsp. saeculare	strain=LMG 14934	GCA_000741375.1	78257	78448	type	True	79.551	307	916	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	79.5203	310	916	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.1266	308	916	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.6375	221	916	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.6933	64	916	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	75.5719	75	916	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	75.3537	50	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:54,888] [INFO] DFAST Taxonomy check result was written to GCF_000741775.1_Bifsub_genomic.fna/tc_result.tsv
[2024-01-25 20:15:54,889] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:54,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:54,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference/checkm_data
[2024-01-25 20:15:54,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:54,919] [INFO] Task started: CheckM
[2024-01-25 20:15:54,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741775.1_Bifsub_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741775.1_Bifsub_genomic.fna/checkm_input GCF_000741775.1_Bifsub_genomic.fna/checkm_result
[2024-01-25 20:16:21,315] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:21,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:21,334] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:21,334] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:21,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741775.1_Bifsub_genomic.fna/markers.fasta)
[2024-01-25 20:16:21,335] [INFO] Task started: Blastn
[2024-01-25 20:16:21,336] [INFO] Running command: blastn -query GCF_000741775.1_Bifsub_genomic.fna/markers.fasta -db /var/lib/cwl/stg73eb9160-a3cf-4a26-b3b7-1829df5d419e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741775.1_Bifsub_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:22,722] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:22,725] [INFO] Selected 17 target genomes.
[2024-01-25 20:16:22,726] [INFO] Target genome list was writen to GCF_000741775.1_Bifsub_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:22,739] [INFO] Task started: fastANI
[2024-01-25 20:16:22,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2dff3e3-8546-4ae6-b0ef-2fdee55dcd79/GCF_000741775.1_Bifsub_genomic.fna.gz --refList GCF_000741775.1_Bifsub_genomic.fna/target_genomes_gtdb.txt --output GCF_000741775.1_Bifsub_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:31,349] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:31,359] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:31,359] [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_000741775.1	s__Bifidobacterium subtile	100.0	915	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	conclusive
GCF_009371885.1	s__Bifidobacterium tibiigranuli	89.4504	680	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000741285.1	s__Bifidobacterium mongoliense	79.879	292	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.8634	358	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000771405.1	s__Bifidobacterium pullorum	79.7435	298	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_012932365.1	s__Bifidobacterium sp012932365	79.67	297	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	79.6105	321	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299505.1	s__Bifidobacterium ramosum	79.4587	310	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	79.4567	303	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_009299475.1	s__Bifidobacterium avesanii	79.3994	300	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018555355.1	s__Bifidobacterium sp018555355	79.3682	303	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_003952945.1	s__Bifidobacterium samirii	79.3629	301	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	79.3344	302	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	79.2126	310	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009078285.1	s__Bifidobacterium jacchi	79.0203	268	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860355.1	s__Galliscardovia margollesii	78.9264	230	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771225.1	s__Bifidobacterium pseudolongum	78.5801	225	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.10	98.38	0.94	0.92	10	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:31,362] [INFO] GTDB search result was written to GCF_000741775.1_Bifsub_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:31,362] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:31,366] [INFO] DFAST_QC result json was written to GCF_000741775.1_Bifsub_genomic.fna/dqc_result.json
[2024-01-25 20:16:31,366] [INFO] DFAST_QC completed!
[2024-01-25 20:16:31,366] [INFO] Total running time: 0h0m56s