[2024-01-24 11:19:54,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:54,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:54,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference
[2024-01-24 11:19:56,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,293] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,293] [INFO] Running command: gunzip -c /var/lib/cwl/stge0905373-0332-46e5-a374-3c96c6c2284a/GCF_003952005.1_ASM395200v1_genomic.fna.gz | prodigal -d GCF_003952005.1_ASM395200v1_genomic.fna/cds.fna -a GCF_003952005.1_ASM395200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:05,897] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:05,898] [INFO] Task started: HMMsearch
[2024-01-24 11:20:05,898] [INFO] Running command: hmmsearch --tblout GCF_003952005.1_ASM395200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference/reference_markers.hmm GCF_003952005.1_ASM395200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:06,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:06,138] [INFO] Found 6/6 markers.
[2024-01-24 11:20:06,179] [INFO] Query marker FASTA was written to GCF_003952005.1_ASM395200v1_genomic.fna/markers.fasta
[2024-01-24 11:20:06,180] [INFO] Task started: Blastn
[2024-01-24 11:20:06,180] [INFO] Running command: blastn -query GCF_003952005.1_ASM395200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference/reference_markers.fasta -out GCF_003952005.1_ASM395200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:07,183] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:07,188] [INFO] Selected 14 target genomes.
[2024-01-24 11:20:07,188] [INFO] Target genome list was writen to GCF_003952005.1_ASM395200v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:07,197] [INFO] Task started: fastANI
[2024-01-24 11:20:07,197] [INFO] Running command: fastANI --query /var/lib/cwl/stge0905373-0332-46e5-a374-3c96c6c2284a/GCF_003952005.1_ASM395200v1_genomic.fna.gz --refList GCF_003952005.1_ASM395200v1_genomic.fna/target_genomes.txt --output GCF_003952005.1_ASM395200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:15,968] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:15,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:15,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:15,980] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:15,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:15,981] [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 callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	100.0	967	971	95	conclusive
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	92.7536	826	971	95	below_threshold
Bifidobacterium tissieri	strain=DSM 100201	GCA_002259645.1	1630162	1630162	type	True	87.4155	723	971	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	84.3457	590	971	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	84.293	602	971	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	83.9821	558	971	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	83.6197	556	971	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	83.3004	492	971	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	81.359	389	971	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.3542	414	971	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.3418	420	971	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.3629	242	971	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	76.1844	57	971	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.1283	82	971	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:15,982] [INFO] DFAST Taxonomy check result was written to GCF_003952005.1_ASM395200v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:15,983] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:15,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:15,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference/checkm_data
[2024-01-24 11:20:15,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:16,021] [INFO] Task started: CheckM
[2024-01-24 11:20:16,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003952005.1_ASM395200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003952005.1_ASM395200v1_genomic.fna/checkm_input GCF_003952005.1_ASM395200v1_genomic.fna/checkm_result
[2024-01-24 11:20:49,281] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:49,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:49,304] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:49,304] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:49,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003952005.1_ASM395200v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:49,305] [INFO] Task started: Blastn
[2024-01-24 11:20:49,305] [INFO] Running command: blastn -query GCF_003952005.1_ASM395200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg161f90ab-804f-4cd8-80e6-0d1db28b58a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003952005.1_ASM395200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:50,631] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:50,634] [INFO] Selected 8 target genomes.
[2024-01-24 11:20:50,634] [INFO] Target genome list was writen to GCF_003952005.1_ASM395200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:50,641] [INFO] Task started: fastANI
[2024-01-24 11:20:50,641] [INFO] Running command: fastANI --query /var/lib/cwl/stge0905373-0332-46e5-a374-3c96c6c2284a/GCF_003952005.1_ASM395200v1_genomic.fna.gz --refList GCF_003952005.1_ASM395200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003952005.1_ASM395200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:56,292] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:56,304] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:56,304] [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_003952005.1	s__Galliscardovia callimiconis	100.0	967	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	conclusive
GCF_002234915.1	s__Galliscardovia vansinderenii	92.7755	825	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259645.1	s__Galliscardovia tissieri	87.4155	723	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	96.74	96.02	0.89	0.88	4	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	84.3642	591	971	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	84.2997	601	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	83.6641	553	971	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	83.3309	490	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667685.1	s__Bifidobacterium aerophilum	81.3556	389	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,306] [INFO] GTDB search result was written to GCF_003952005.1_ASM395200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:56,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:56,309] [INFO] DFAST_QC result json was written to GCF_003952005.1_ASM395200v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:56,310] [INFO] DFAST_QC completed!
[2024-01-24 11:20:56,310] [INFO] Total running time: 0h1m1s