[2024-01-25 17:49:35,661] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:35,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:35,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference
[2024-01-25 17:49:36,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:36,798] [INFO] Task started: Prodigal
[2024-01-25 17:49:36,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg766fc99e-b3fa-42c1-9649-f14726e97fac/GCF_900148495.1_PRJEB16359_genomic.fna.gz | prodigal -d GCF_900148495.1_PRJEB16359_genomic.fna/cds.fna -a GCF_900148495.1_PRJEB16359_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:43,652] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:43,653] [INFO] Task started: HMMsearch
[2024-01-25 17:49:43,653] [INFO] Running command: hmmsearch --tblout GCF_900148495.1_PRJEB16359_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference/reference_markers.hmm GCF_900148495.1_PRJEB16359_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:43,861] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:43,863] [INFO] Found 6/6 markers.
[2024-01-25 17:49:43,885] [INFO] Query marker FASTA was written to GCF_900148495.1_PRJEB16359_genomic.fna/markers.fasta
[2024-01-25 17:49:43,885] [INFO] Task started: Blastn
[2024-01-25 17:49:43,886] [INFO] Running command: blastn -query GCF_900148495.1_PRJEB16359_genomic.fna/markers.fasta -db /var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference/reference_markers.fasta -out GCF_900148495.1_PRJEB16359_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:44,464] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:44,467] [INFO] Selected 22 target genomes.
[2024-01-25 17:49:44,467] [INFO] Target genome list was writen to GCF_900148495.1_PRJEB16359_genomic.fna/target_genomes.txt
[2024-01-25 17:49:44,489] [INFO] Task started: fastANI
[2024-01-25 17:49:44,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg766fc99e-b3fa-42c1-9649-f14726e97fac/GCF_900148495.1_PRJEB16359_genomic.fna.gz --refList GCF_900148495.1_PRJEB16359_genomic.fna/target_genomes.txt --output GCF_900148495.1_PRJEB16359_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:57,905] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:57,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:57,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:57,910] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:57,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:57,910] [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
Negativibacillus massiliensis	strain=Marseille-P3213	GCA_900148495.1	1871035	1871035	type	True	100.0	956	957	95	conclusive
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	87.2358	58	957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:57,911] [INFO] DFAST Taxonomy check result was written to GCF_900148495.1_PRJEB16359_genomic.fna/tc_result.tsv
[2024-01-25 17:49:57,911] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:57,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:57,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference/checkm_data
[2024-01-25 17:49:57,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:57,941] [INFO] Task started: CheckM
[2024-01-25 17:49:57,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900148495.1_PRJEB16359_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900148495.1_PRJEB16359_genomic.fna/checkm_input GCF_900148495.1_PRJEB16359_genomic.fna/checkm_result
[2024-01-25 17:50:22,830] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:22,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:22,850] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:22,850] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:22,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900148495.1_PRJEB16359_genomic.fna/markers.fasta)
[2024-01-25 17:50:22,851] [INFO] Task started: Blastn
[2024-01-25 17:50:22,851] [INFO] Running command: blastn -query GCF_900148495.1_PRJEB16359_genomic.fna/markers.fasta -db /var/lib/cwl/stg88f4c824-3cc1-4d07-ae78-cd73df20977e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900148495.1_PRJEB16359_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:23,898] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:23,901] [INFO] Selected 19 target genomes.
[2024-01-25 17:50:23,901] [INFO] Target genome list was writen to GCF_900148495.1_PRJEB16359_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:23,942] [INFO] Task started: fastANI
[2024-01-25 17:50:23,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg766fc99e-b3fa-42c1-9649-f14726e97fac/GCF_900148495.1_PRJEB16359_genomic.fna.gz --refList GCF_900148495.1_PRJEB16359_genomic.fna/target_genomes_gtdb.txt --output GCF_900148495.1_PRJEB16359_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:31,614] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:31,620] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:31,620] [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_900148495.1	s__Negativibacillus massiliensis	100.0	956	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.84	97.23	0.93	0.91	5	conclusive
GCF_900104675.1	s__Angelakisella massiliensis	87.0185	59	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197685.1	s__Negativibacillus sp905197685	79.5863	322	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435195.1	s__Negativibacillus sp000435195	79.4822	279	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	98.99	98.94	0.90	0.88	5	-
GCA_900547015.1	s__Negativibacillus sp900547015	79.463	213	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.91	97.91	0.85	0.85	2	-
GCA_900547455.1	s__Negativibacillus faecipullorum	78.7139	237	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.80	97.60	0.92	0.88	7	-
GCA_017848075.1	s__Negativibacillus sp017848075	78.3475	65	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017439985.1	s__Negativibacillus sp017439985	78.2593	99	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	96.97	96.97	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:31,623] [INFO] GTDB search result was written to GCF_900148495.1_PRJEB16359_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:31,623] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:31,626] [INFO] DFAST_QC result json was written to GCF_900148495.1_PRJEB16359_genomic.fna/dqc_result.json
[2024-01-25 17:50:31,626] [INFO] DFAST_QC completed!
[2024-01-25 17:50:31,626] [INFO] Total running time: 0h0m56s