[2024-01-25 20:05:50,733] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:50,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:50,734] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference
[2024-01-25 20:05:51,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:51,852] [INFO] Task started: Prodigal
[2024-01-25 20:05:51,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b012e6-4ad0-4606-99e0-5c74e09e249d/GCF_014191315.1_ASM1419131v1_genomic.fna.gz | prodigal -d GCF_014191315.1_ASM1419131v1_genomic.fna/cds.fna -a GCF_014191315.1_ASM1419131v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:56,029] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:56,030] [INFO] Task started: HMMsearch
[2024-01-25 20:05:56,030] [INFO] Running command: hmmsearch --tblout GCF_014191315.1_ASM1419131v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference/reference_markers.hmm GCF_014191315.1_ASM1419131v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:56,242] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:56,243] [INFO] Found 6/6 markers.
[2024-01-25 20:05:56,259] [INFO] Query marker FASTA was written to GCF_014191315.1_ASM1419131v1_genomic.fna/markers.fasta
[2024-01-25 20:05:56,259] [INFO] Task started: Blastn
[2024-01-25 20:05:56,259] [INFO] Running command: blastn -query GCF_014191315.1_ASM1419131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference/reference_markers.fasta -out GCF_014191315.1_ASM1419131v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:56,937] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:56,939] [INFO] Selected 16 target genomes.
[2024-01-25 20:05:56,940] [INFO] Target genome list was writen to GCF_014191315.1_ASM1419131v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:56,947] [INFO] Task started: fastANI
[2024-01-25 20:05:56,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b012e6-4ad0-4606-99e0-5c74e09e249d/GCF_014191315.1_ASM1419131v1_genomic.fna.gz --refList GCF_014191315.1_ASM1419131v1_genomic.fna/target_genomes.txt --output GCF_014191315.1_ASM1419131v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:03,673] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:03,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:03,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:03,684] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:06:03,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:03,684] [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 commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	100.0	482	488	95	conclusive
Bifidobacterium commune	strain=R-52791	GCA_900094885.1	1505727	1505727	type	True	99.9911	473	488	95	conclusive
Bifidobacterium bohemicum	strain=DSM 22767	GCA_000741525.1	638617	638617	type	True	78.2099	116	488	95	below_threshold
Bifidobacterium bohemicum	strain=DSM 22767	GCA_000771605.1	638617	638617	type	True	78.0174	117	488	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=JCM 1200	GCA_001025215.1	28026	28026	type	True	78.0154	91	488	95	below_threshold
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	77.8152	89	488	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000173435.1	28026	28026	type	True	77.7586	92	488	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	77.7404	80	488	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	77.7257	89	488	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	77.6735	88	488	95	below_threshold
Bifidobacterium saguini	strain=DSMZ 23967	GCA_017378515.1	762210	762210	type	True	77.6699	80	488	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	77.5925	87	488	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000770925.1	78346	78346	type	True	77.4564	88	488	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	77.3567	83	488	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	76.8176	50	488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:03,686] [INFO] DFAST Taxonomy check result was written to GCF_014191315.1_ASM1419131v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:03,686] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:03,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:03,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference/checkm_data
[2024-01-25 20:06:03,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:03,708] [INFO] Task started: CheckM
[2024-01-25 20:06:03,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191315.1_ASM1419131v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191315.1_ASM1419131v1_genomic.fna/checkm_input GCF_014191315.1_ASM1419131v1_genomic.fna/checkm_result
[2024-01-25 20:06:22,360] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:22,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:22,397] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:22,397] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:22,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191315.1_ASM1419131v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:22,397] [INFO] Task started: Blastn
[2024-01-25 20:06:22,398] [INFO] Running command: blastn -query GCF_014191315.1_ASM1419131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc67dba-427b-41f7-8f70-b02d8b89c4ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191315.1_ASM1419131v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:23,382] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:23,385] [INFO] Selected 25 target genomes.
[2024-01-25 20:06:23,385] [INFO] Target genome list was writen to GCF_014191315.1_ASM1419131v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:23,401] [INFO] Task started: fastANI
[2024-01-25 20:06:23,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b012e6-4ad0-4606-99e0-5c74e09e249d/GCF_014191315.1_ASM1419131v1_genomic.fna.gz --refList GCF_014191315.1_ASM1419131v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191315.1_ASM1419131v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:33,188] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:33,199] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:33,199] [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_900094885.1	s__Bifidobacterium commune	99.9911	473	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.97	0.97	2	conclusive
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	78.1783	92	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_000741525.1	s__Bifidobacterium bohemicum	78.1781	117	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000522505.1	s__Bifidobacterium moukalabense	77.9032	89	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_001025135.1	s__Bifidobacterium bifidum	77.872	92	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	-
GCF_001042595.1	s__Bifidobacterium dentium	77.7395	82	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_000741715.1	s__Bifidobacterium saguini	77.7092	78	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	-
GCF_002286935.1	s__Bifidobacterium criceti	77.676	57	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.26	97.26	0.94	0.94	2	-
GCF_018555335.1	s__Bifidobacterium sp018555335	77.5502	79	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000771265.1	s__Bifidobacterium thermophilum	77.4795	73	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_000770925.1	s__Bifidobacterium ruminantium	77.4564	88	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_000771225.1	s__Bifidobacterium pseudolongum	77.3848	63	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.10	98.38	0.94	0.92	10	-
GCF_018555635.1	s__Bifidobacterium sp018555635	77.3391	79	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737845.1	s__Bifidobacterium bombi	77.2925	90	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002451435.1	s__Bifidobacterium sp002451435	77.2629	80	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000499285.1	s__Bifidobacterium sp000499285	77.1139	50	488	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	77.1107	87	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009078285.1	s__Bifidobacterium jacchi	76.9562	84	488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:33,201] [INFO] GTDB search result was written to GCF_014191315.1_ASM1419131v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:33,202] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:33,205] [INFO] DFAST_QC result json was written to GCF_014191315.1_ASM1419131v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:33,206] [INFO] DFAST_QC completed!
[2024-01-25 20:06:33,206] [INFO] Total running time: 0h0m42s