[2024-01-24 11:43:25,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference
[2024-01-24 11:43:30,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,058] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c63ad62-40d9-4037-9b44-66194dd5681b/GCF_014384995.1_ASM1438499v1_genomic.fna.gz | prodigal -d GCF_014384995.1_ASM1438499v1_genomic.fna/cds.fna -a GCF_014384995.1_ASM1438499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:36,776] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:36,776] [INFO] Task started: HMMsearch
[2024-01-24 11:43:36,776] [INFO] Running command: hmmsearch --tblout GCF_014384995.1_ASM1438499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference/reference_markers.hmm GCF_014384995.1_ASM1438499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:37,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:37,054] [INFO] Found 6/6 markers.
[2024-01-24 11:43:37,087] [INFO] Query marker FASTA was written to GCF_014384995.1_ASM1438499v1_genomic.fna/markers.fasta
[2024-01-24 11:43:37,087] [INFO] Task started: Blastn
[2024-01-24 11:43:37,087] [INFO] Running command: blastn -query GCF_014384995.1_ASM1438499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference/reference_markers.fasta -out GCF_014384995.1_ASM1438499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:37,696] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:37,699] [INFO] Selected 16 target genomes.
[2024-01-24 11:43:37,700] [INFO] Target genome list was writen to GCF_014384995.1_ASM1438499v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:37,706] [INFO] Task started: fastANI
[2024-01-24 11:43:37,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c63ad62-40d9-4037-9b44-66194dd5681b/GCF_014384995.1_ASM1438499v1_genomic.fna.gz --refList GCF_014384995.1_ASM1438499v1_genomic.fna/target_genomes.txt --output GCF_014384995.1_ASM1438499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:45,351] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:45,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:45,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:45,359] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:43:45,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:43:45,360] [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
Cellulosilyticum ruminicola	strain=JCM 14822	GCA_001311925.1	425254	425254	type	True	78.1642	154	1253	95	below_threshold
Cellulosilyticum lentocellum	strain=DSM 5427	GCA_000178835.2	29360	29360	type	True	77.8651	181	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:45,363] [INFO] DFAST Taxonomy check result was written to GCF_014384995.1_ASM1438499v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:45,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:45,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:45,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference/checkm_data
[2024-01-24 11:43:45,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:45,404] [INFO] Task started: CheckM
[2024-01-24 11:43:45,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384995.1_ASM1438499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384995.1_ASM1438499v1_genomic.fna/checkm_input GCF_014384995.1_ASM1438499v1_genomic.fna/checkm_result
[2024-01-24 11:44:11,805] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:11,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:11,828] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:11,828] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:11,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384995.1_ASM1438499v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:11,829] [INFO] Task started: Blastn
[2024-01-24 11:44:11,829] [INFO] Running command: blastn -query GCF_014384995.1_ASM1438499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd00ab186-dd67-4da6-b8a0-53de579328fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384995.1_ASM1438499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:12,850] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:12,853] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:12,853] [INFO] Target genome list was writen to GCF_014384995.1_ASM1438499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:12,867] [INFO] Task started: fastANI
[2024-01-24 11:44:12,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c63ad62-40d9-4037-9b44-66194dd5681b/GCF_014384995.1_ASM1438499v1_genomic.fna.gz --refList GCF_014384995.1_ASM1438499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384995.1_ASM1438499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:21,153] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:21,167] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:21,168] [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
GCA_014384995.1	s__Niameybacter stercoravium	100.0	1246	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	97.76	95.05	0.90	0.86	8	conclusive
GCA_017941635.1	s__Cellulosilyticum sp017941635	81.5992	158	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282685.1	s__Niameybacter massiliensis	80.5909	524	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551325.1	s__Niameybacter sp900551325	79.818	473	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058045.1	s__Cellulosilyticum sp015058045	78.2773	147	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311925.1	s__Cellulosilyticum ruminicola	78.1755	155	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178835.2	s__Cellulosilyticum lentocellum	77.8439	180	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	97.43	97.43	0.84	0.84	2	-
GCA_017421915.1	s__Cellulosilyticum sp017421915	77.8361	103	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002735925.1	s__Cellulosilyticum sp002735925	77.5646	147	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883705.1	s__Cellulosilyticum pullistercoris	77.5294	108	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095725.1	s__FMMP01 sp900095725	77.2847	112	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__FMMP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002007365.1	s__Epulopiscium_D sp002007365	77.0939	63	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Epulopiscium_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:21,169] [INFO] GTDB search result was written to GCF_014384995.1_ASM1438499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:21,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:21,287] [INFO] DFAST_QC result json was written to GCF_014384995.1_ASM1438499v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:21,287] [INFO] DFAST_QC completed!
[2024-01-24 11:44:21,287] [INFO] Total running time: 0h0m56s