[2024-01-24 14:06:14,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,667] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference
[2024-01-24 14:06:15,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:15,997] [INFO] Task started: Prodigal
[2024-01-24 14:06:15,998] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e2eb593-fe47-4aae-913a-5f6427766b25/GCF_019331675.1_ASM1933167v1_genomic.fna.gz | prodigal -d GCF_019331675.1_ASM1933167v1_genomic.fna/cds.fna -a GCF_019331675.1_ASM1933167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:25,786] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:25,787] [INFO] Task started: HMMsearch
[2024-01-24 14:06:25,787] [INFO] Running command: hmmsearch --tblout GCF_019331675.1_ASM1933167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference/reference_markers.hmm GCF_019331675.1_ASM1933167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:26,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:26,078] [INFO] Found 6/6 markers.
[2024-01-24 14:06:26,118] [INFO] Query marker FASTA was written to GCF_019331675.1_ASM1933167v1_genomic.fna/markers.fasta
[2024-01-24 14:06:26,119] [INFO] Task started: Blastn
[2024-01-24 14:06:26,119] [INFO] Running command: blastn -query GCF_019331675.1_ASM1933167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference/reference_markers.fasta -out GCF_019331675.1_ASM1933167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:27,219] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:27,223] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:27,223] [INFO] Target genome list was writen to GCF_019331675.1_ASM1933167v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:27,231] [INFO] Task started: fastANI
[2024-01-24 14:06:27,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2eb593-fe47-4aae-913a-5f6427766b25/GCF_019331675.1_ASM1933167v1_genomic.fna.gz --refList GCF_019331675.1_ASM1933167v1_genomic.fna/target_genomes.txt --output GCF_019331675.1_ASM1933167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:35,333] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:35,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:35,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:35,347] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:35,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:35,348] [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 miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	100.0	970	974	95	conclusive
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	93.6973	762	974	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	86.4468	674	974	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	84.3799	510	974	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	84.3784	510	974	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	84.3003	495	974	95	below_threshold
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	84.2991	502	974	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	84.2123	511	974	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	84.159	476	974	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	84.1438	491	974	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	83.2762	521	974	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.5121	293	974	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.3324	198	974	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.0072	104	974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:35,349] [INFO] DFAST Taxonomy check result was written to GCF_019331675.1_ASM1933167v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:35,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:35,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:35,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference/checkm_data
[2024-01-24 14:06:35,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:35,385] [INFO] Task started: CheckM
[2024-01-24 14:06:35,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019331675.1_ASM1933167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019331675.1_ASM1933167v1_genomic.fna/checkm_input GCF_019331675.1_ASM1933167v1_genomic.fna/checkm_result
[2024-01-24 14:07:08,266] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:08,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:08,292] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:08,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:08,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019331675.1_ASM1933167v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:08,293] [INFO] Task started: Blastn
[2024-01-24 14:07:08,294] [INFO] Running command: blastn -query GCF_019331675.1_ASM1933167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd7f2d6-e593-4be0-ad68-a89fa350f41e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019331675.1_ASM1933167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:09,919] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:09,922] [INFO] Selected 9 target genomes.
[2024-01-24 14:07:09,922] [INFO] Target genome list was writen to GCF_019331675.1_ASM1933167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:09,932] [INFO] Task started: fastANI
[2024-01-24 14:07:09,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2eb593-fe47-4aae-913a-5f6427766b25/GCF_019331675.1_ASM1933167v1_genomic.fna.gz --refList GCF_019331675.1_ASM1933167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019331675.1_ASM1933167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:15,592] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:15,602] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:15,602] [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_018555355.1	s__Bifidobacterium sp018555355	96.2048	815	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	conclusive
GCF_003129905.1	s__Bifidobacterium callitrichidarum	93.7005	761	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259745.1	s__Bifidobacterium myosotis	86.4432	674	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_000196555.1	s__Bifidobacterium longum	84.3583	511	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_000269965.1	s__Bifidobacterium infantis	84.1345	493	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_000741695.1	s__Bifidobacterium reuteri	83.8785	562	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_001025175.1	s__Bifidobacterium breve	83.2545	473	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_009299475.1	s__Bifidobacterium avesanii	83.1784	471	974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:15,604] [INFO] GTDB search result was written to GCF_019331675.1_ASM1933167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:15,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:15,609] [INFO] DFAST_QC result json was written to GCF_019331675.1_ASM1933167v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:15,610] [INFO] DFAST_QC completed!
[2024-01-24 14:07:15,610] [INFO] Total running time: 0h1m1s