[2023-06-13 18:26:31,529] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:26:31,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:26:31,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference
[2023-06-13 18:26:32,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:26:32,695] [INFO] Task started: Prodigal
[2023-06-13 18:26:32,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg677909b7-20d5-4076-861b-6c6f80800d73/GCA_022648265.1_ASM2264826v1_genomic.fna.gz | prodigal -d GCA_022648265.1_ASM2264826v1_genomic.fna/cds.fna -a GCA_022648265.1_ASM2264826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:26:40,667] [INFO] Task succeeded: Prodigal
[2023-06-13 18:26:40,667] [INFO] Task started: HMMsearch
[2023-06-13 18:26:40,667] [INFO] Running command: hmmsearch --tblout GCA_022648265.1_ASM2264826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference/reference_markers.hmm GCA_022648265.1_ASM2264826v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:26:40,848] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:26:40,850] [INFO] Found 6/6 markers.
[2023-06-13 18:26:40,873] [INFO] Query marker FASTA was written to GCA_022648265.1_ASM2264826v1_genomic.fna/markers.fasta
[2023-06-13 18:26:40,873] [INFO] Task started: Blastn
[2023-06-13 18:26:40,873] [INFO] Running command: blastn -query GCA_022648265.1_ASM2264826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference/reference_markers.fasta -out GCA_022648265.1_ASM2264826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:26:41,732] [INFO] Task succeeded: Blastn
[2023-06-13 18:26:41,735] [INFO] Selected 10 target genomes.
[2023-06-13 18:26:41,735] [INFO] Target genome list was writen to GCA_022648265.1_ASM2264826v1_genomic.fna/target_genomes.txt
[2023-06-13 18:26:41,736] [INFO] Task started: fastANI
[2023-06-13 18:26:41,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg677909b7-20d5-4076-861b-6c6f80800d73/GCA_022648265.1_ASM2264826v1_genomic.fna.gz --refList GCA_022648265.1_ASM2264826v1_genomic.fna/target_genomes.txt --output GCA_022648265.1_ASM2264826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:26:47,449] [INFO] Task succeeded: fastANI
[2023-06-13 18:26:47,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:26:47,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:26:47,459] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 18:26:47,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 18:26:47,459] [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 tibiigranuli	strain=TMW 2.2057	GCA_009371885.1	2172043	2172043	type	True	95.6249	682	835	95	conclusive
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	89.387	619	835	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	89.3787	617	835	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	89.367	631	835	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.9511	288	835	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	79.7155	313	835	95	below_threshold
Bifidobacterium mongoliense	strain=DSM 21395	GCA_000771525.1	518643	518643	type	True	79.5261	265	835	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	79.3844	268	835	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	79.2997	265	835	95	below_threshold
Bifidobacterium avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	79.2896	270	835	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:26:47,461] [INFO] DFAST Taxonomy check result was written to GCA_022648265.1_ASM2264826v1_genomic.fna/tc_result.tsv
[2023-06-13 18:26:47,461] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:26:47,461] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:26:47,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference/checkm_data
[2023-06-13 18:26:47,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:26:47,488] [INFO] Task started: CheckM
[2023-06-13 18:26:47,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022648265.1_ASM2264826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022648265.1_ASM2264826v1_genomic.fna/checkm_input GCA_022648265.1_ASM2264826v1_genomic.fna/checkm_result
[2023-06-13 18:27:14,950] [INFO] Task succeeded: CheckM
[2023-06-13 18:27:14,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:27:14,971] [INFO] ===== Completeness check finished =====
[2023-06-13 18:27:14,971] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:27:14,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022648265.1_ASM2264826v1_genomic.fna/markers.fasta)
[2023-06-13 18:27:14,972] [INFO] Task started: Blastn
[2023-06-13 18:27:14,972] [INFO] Running command: blastn -query GCA_022648265.1_ASM2264826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d0f3624-dde6-4957-a540-6e6239fff4ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_022648265.1_ASM2264826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:27:16,235] [INFO] Task succeeded: Blastn
[2023-06-13 18:27:16,240] [INFO] Selected 16 target genomes.
[2023-06-13 18:27:16,240] [INFO] Target genome list was writen to GCA_022648265.1_ASM2264826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:27:16,242] [INFO] Task started: fastANI
[2023-06-13 18:27:16,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg677909b7-20d5-4076-861b-6c6f80800d73/GCA_022648265.1_ASM2264826v1_genomic.fna.gz --refList GCA_022648265.1_ASM2264826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022648265.1_ASM2264826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:27:24,146] [INFO] Task succeeded: fastANI
[2023-06-13 18:27:24,159] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:27:24,160] [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_009371885.1	s__Bifidobacterium tibiigranuli	95.5944	683	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000741775.1	s__Bifidobacterium subtile	89.3756	629	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_001042635.1	s__Bifidobacterium scardovii	80.104	284	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_018555385.1	s__Bifidobacterium sp018555385	79.6122	275	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741285.1	s__Bifidobacterium mongoliense	79.5524	259	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	79.4888	255	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_009299505.1	s__Bifidobacterium ramosum	79.4401	281	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014898175.1	s__Bifidobacterium lemurum	79.3967	275	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.3872	260	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	79.3824	266	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.3493	270	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555355.1	s__Bifidobacterium sp018555355	79.3147	273	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_009299475.1	s__Bifidobacterium avesanii	79.2828	271	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	79.2237	303	835	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	79.1246	272	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.0824	236	835	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
--------------------------------------------------------------------------------
[2023-06-13 18:27:24,162] [INFO] GTDB search result was written to GCA_022648265.1_ASM2264826v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:27:24,163] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:27:24,167] [INFO] DFAST_QC result json was written to GCA_022648265.1_ASM2264826v1_genomic.fna/dqc_result.json
[2023-06-13 18:27:24,167] [INFO] DFAST_QC completed!
[2023-06-13 18:27:24,167] [INFO] Total running time: 0h0m53s