[2024-01-24 10:57:05,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:05,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:05,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference
[2024-01-24 10:57:06,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:06,534] [INFO] Task started: Prodigal
[2024-01-24 10:57:06,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg56ef90ab-c3b4-4667-b8f8-560dfe8cf346/GCF_003609635.1_ASM360963v1_genomic.fna.gz | prodigal -d GCF_003609635.1_ASM360963v1_genomic.fna/cds.fna -a GCF_003609635.1_ASM360963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:16,677] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:16,678] [INFO] Task started: HMMsearch
[2024-01-24 10:57:16,678] [INFO] Running command: hmmsearch --tblout GCF_003609635.1_ASM360963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference/reference_markers.hmm GCF_003609635.1_ASM360963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:16,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:16,964] [INFO] Found 6/6 markers.
[2024-01-24 10:57:17,004] [INFO] Query marker FASTA was written to GCF_003609635.1_ASM360963v1_genomic.fna/markers.fasta
[2024-01-24 10:57:17,004] [INFO] Task started: Blastn
[2024-01-24 10:57:17,005] [INFO] Running command: blastn -query GCF_003609635.1_ASM360963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference/reference_markers.fasta -out GCF_003609635.1_ASM360963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:17,652] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:17,656] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:17,657] [INFO] Target genome list was writen to GCF_003609635.1_ASM360963v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:17,665] [INFO] Task started: fastANI
[2024-01-24 10:57:17,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ef90ab-c3b4-4667-b8f8-560dfe8cf346/GCF_003609635.1_ASM360963v1_genomic.fna.gz --refList GCF_003609635.1_ASM360963v1_genomic.fna/target_genomes.txt --output GCF_003609635.1_ASM360963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:31,780] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:31,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:31,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:31,789] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:31,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:31,789] [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
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	100.0	1526	1529	95	conclusive
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	83.6112	1118	1529	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	78.971	440	1529	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	78.7393	460	1529	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	78.6983	456	1529	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.8591	187	1529	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	77.7876	167	1529	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.778	182	1529	95	below_threshold
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	76.8337	59	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:31,792] [INFO] DFAST Taxonomy check result was written to GCF_003609635.1_ASM360963v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:31,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:31,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:31,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference/checkm_data
[2024-01-24 10:57:31,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:31,846] [INFO] Task started: CheckM
[2024-01-24 10:57:31,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003609635.1_ASM360963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003609635.1_ASM360963v1_genomic.fna/checkm_input GCF_003609635.1_ASM360963v1_genomic.fna/checkm_result
[2024-01-24 10:58:06,533] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:06,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:06,567] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:06,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:06,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003609635.1_ASM360963v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:06,568] [INFO] Task started: Blastn
[2024-01-24 10:58:06,568] [INFO] Running command: blastn -query GCF_003609635.1_ASM360963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95e3a2f8-0cae-44b5-9143-81d2439a091b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003609635.1_ASM360963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:07,644] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:07,648] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:07,649] [INFO] Target genome list was writen to GCF_003609635.1_ASM360963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:07,658] [INFO] Task started: fastANI
[2024-01-24 10:58:07,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ef90ab-c3b4-4667-b8f8-560dfe8cf346/GCF_003609635.1_ASM360963v1_genomic.fna.gz --refList GCF_003609635.1_ASM360963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003609635.1_ASM360963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:17,445] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:17,461] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:17,461] [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_003609635.1	s__Lacrimispora algidixylanolytica	100.0	1526	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002478865.1	s__Lacrimispora sp002478865	94.4045	876	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.36	98.36	0.73	0.73	2	-
GCF_000687555.1	s__Lacrimispora aerotolerans	83.6213	1116	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526575.1	s__Lacrimispora sp000526575	83.5296	1102	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.63	98.56	0.93	0.92	3	-
GCA_905215155.1	s__Lacrimispora sp905215155	80.3259	628	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007115105.1	s__Lacrimispora sp007115105	79.7865	554	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205965.1	s__Lacrimispora amygdalina_A	79.3242	474	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367105.1	s__Lacrimispora sp002367105	78.7172	451	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201875.1	s__Hungatella effluvii	77.7989	181	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	95.81	95.49	0.78	0.75	20	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,473] [INFO] GTDB search result was written to GCF_003609635.1_ASM360963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:17,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:17,482] [INFO] DFAST_QC result json was written to GCF_003609635.1_ASM360963v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:17,482] [INFO] DFAST_QC completed!
[2024-01-24 10:58:17,483] [INFO] Total running time: 0h1m12s