[2024-01-24 14:23:20,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference
[2024-01-24 14:23:21,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:21,857] [INFO] Task started: Prodigal
[2024-01-24 14:23:21,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg91fe1b02-6b19-4a61-9952-9c5cc833926a/GCF_002860355.1_ASM286035v1_genomic.fna.gz | prodigal -d GCF_002860355.1_ASM286035v1_genomic.fna/cds.fna -a GCF_002860355.1_ASM286035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:31,145] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:31,145] [INFO] Task started: HMMsearch
[2024-01-24 14:23:31,145] [INFO] Running command: hmmsearch --tblout GCF_002860355.1_ASM286035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference/reference_markers.hmm GCF_002860355.1_ASM286035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:31,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:31,443] [INFO] Found 6/6 markers.
[2024-01-24 14:23:31,476] [INFO] Query marker FASTA was written to GCF_002860355.1_ASM286035v1_genomic.fna/markers.fasta
[2024-01-24 14:23:31,477] [INFO] Task started: Blastn
[2024-01-24 14:23:31,477] [INFO] Running command: blastn -query GCF_002860355.1_ASM286035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference/reference_markers.fasta -out GCF_002860355.1_ASM286035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:32,488] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:32,492] [INFO] Selected 17 target genomes.
[2024-01-24 14:23:32,493] [INFO] Target genome list was writen to GCF_002860355.1_ASM286035v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:32,525] [INFO] Task started: fastANI
[2024-01-24 14:23:32,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg91fe1b02-6b19-4a61-9952-9c5cc833926a/GCF_002860355.1_ASM286035v1_genomic.fna.gz --refList GCF_002860355.1_ASM286035v1_genomic.fna/target_genomes.txt --output GCF_002860355.1_ASM286035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:44,389] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:44,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:44,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:44,408] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:44,408] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:44,409] [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 margollesii	strain=Uis1B	GCA_002860355.1	2020964	2020964	type	True	100.0	884	886	95	conclusive
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	87.0739	670	886	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	82.9536	488	886	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	82.7391	503	886	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	82.5896	479	886	95	below_threshold
Bifidobacterium callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	82.4111	473	886	95	below_threshold
Bifidobacterium tissieri	strain=DSM 100201	GCA_002259645.1	1630162	1630162	type	True	82.2104	464	886	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.153	356	886	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.9226	355	886	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	80.8522	337	886	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	80.8265	326	886	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	80.7736	333	886	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000770925.1	78346	78346	type	True	80.0002	272	886	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	79.9128	272	886	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.8866	213	886	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.0008	140	886	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.3083	71	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:44,414] [INFO] DFAST Taxonomy check result was written to GCF_002860355.1_ASM286035v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:44,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:44,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:44,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference/checkm_data
[2024-01-24 14:23:44,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:44,456] [INFO] Task started: CheckM
[2024-01-24 14:23:44,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002860355.1_ASM286035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002860355.1_ASM286035v1_genomic.fna/checkm_input GCF_002860355.1_ASM286035v1_genomic.fna/checkm_result
[2024-01-24 14:24:17,922] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:17,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:17,941] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:17,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:17,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002860355.1_ASM286035v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:17,943] [INFO] Task started: Blastn
[2024-01-24 14:24:17,943] [INFO] Running command: blastn -query GCF_002860355.1_ASM286035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a5f6154-2a45-4f68-b37b-ba17cdba1191/dqc_reference/reference_markers_gtdb.fasta -out GCF_002860355.1_ASM286035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:19,324] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:19,327] [INFO] Selected 13 target genomes.
[2024-01-24 14:24:19,327] [INFO] Target genome list was writen to GCF_002860355.1_ASM286035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:19,337] [INFO] Task started: fastANI
[2024-01-24 14:24:19,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg91fe1b02-6b19-4a61-9952-9c5cc833926a/GCF_002860355.1_ASM286035v1_genomic.fna.gz --refList GCF_002860355.1_ASM286035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002860355.1_ASM286035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:26,993] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:27,011] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:27,011] [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_002860355.1	s__Galliscardovia margollesii	100.0	884	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002802905.1	s__Galliscardovia simiarum	87.0925	669	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_003129925.1	s__Galliscardovia catulorum	83.2586	445	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	82.95	490	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002802875.1	s__Galliscardovia primatium	82.7717	501	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234915.1	s__Galliscardovia vansinderenii	82.6052	478	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	82.3829	475	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_002259645.1	s__Galliscardovia tissieri	82.1815	467	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	96.74	96.02	0.89	0.88	4	-
GCF_012932365.1	s__Bifidobacterium sp012932365	81.8588	384	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	80.8386	340	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_009299475.1	s__Bifidobacterium avesanii	80.635	363	886	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	80.4238	282	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_000770925.1	s__Bifidobacterium ruminantium	79.9688	274	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:27,013] [INFO] GTDB search result was written to GCF_002860355.1_ASM286035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:27,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:27,019] [INFO] DFAST_QC result json was written to GCF_002860355.1_ASM286035v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:27,019] [INFO] DFAST_QC completed!
[2024-01-24 14:24:27,019] [INFO] Total running time: 0h1m7s