[2024-01-24 13:57:00,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference
[2024-01-24 13:57:02,330] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,331] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,331] [INFO] Running command: gunzip -c /var/lib/cwl/stgedf104ee-f98f-4043-9b4b-777e62266f93/GCF_000699585.2_CLIT1_genomic.fna.gz | prodigal -d GCF_000699585.2_CLIT1_genomic.fna/cds.fna -a GCF_000699585.2_CLIT1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:10,693] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:10,693] [INFO] Task started: HMMsearch
[2024-01-24 13:57:10,693] [INFO] Running command: hmmsearch --tblout GCF_000699585.2_CLIT1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference/reference_markers.hmm GCF_000699585.2_CLIT1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:11,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:11,031] [INFO] Found 6/6 markers.
[2024-01-24 13:57:11,063] [INFO] Query marker FASTA was written to GCF_000699585.2_CLIT1_genomic.fna/markers.fasta
[2024-01-24 13:57:11,063] [INFO] Task started: Blastn
[2024-01-24 13:57:11,063] [INFO] Running command: blastn -query GCF_000699585.2_CLIT1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference/reference_markers.fasta -out GCF_000699585.2_CLIT1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:11,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:11,702] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:11,702] [INFO] Target genome list was writen to GCF_000699585.2_CLIT1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:11,713] [INFO] Task started: fastANI
[2024-01-24 13:57:11,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgedf104ee-f98f-4043-9b4b-777e62266f93/GCF_000699585.2_CLIT1_genomic.fna.gz --refList GCF_000699585.2_CLIT1_genomic.fna/target_genomes.txt --output GCF_000699585.2_CLIT1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:19,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:19,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:19,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:19,574] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:19,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:19,575] [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
Peptoclostridium litorale	strain=W6	GCA_000699585.2	1557	1557	type	True	100.0	1093	1122	95	conclusive
Peptoclostridium litorale	strain=DSM 5388	GCA_900141635.1	1557	1557	type	True	99.9637	1040	1122	95	conclusive
Peptoclostridium acidaminophilum	strain=DSM 3953	GCA_000597865.1	1731	1731	type	True	78.8453	170	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:19,576] [INFO] DFAST Taxonomy check result was written to GCF_000699585.2_CLIT1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:19,577] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:19,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:19,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference/checkm_data
[2024-01-24 13:57:19,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:19,617] [INFO] Task started: CheckM
[2024-01-24 13:57:19,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000699585.2_CLIT1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000699585.2_CLIT1_genomic.fna/checkm_input GCF_000699585.2_CLIT1_genomic.fna/checkm_result
[2024-01-24 13:57:50,885] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:50,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:50,909] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:50,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:50,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000699585.2_CLIT1_genomic.fna/markers.fasta)
[2024-01-24 13:57:50,910] [INFO] Task started: Blastn
[2024-01-24 13:57:50,910] [INFO] Running command: blastn -query GCF_000699585.2_CLIT1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67933259-9862-4952-ae7e-9953dd5d9b4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000699585.2_CLIT1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:51,859] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:51,863] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:51,864] [INFO] Target genome list was writen to GCF_000699585.2_CLIT1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:51,885] [INFO] Task started: fastANI
[2024-01-24 13:57:51,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgedf104ee-f98f-4043-9b4b-777e62266f93/GCF_000699585.2_CLIT1_genomic.fna.gz --refList GCF_000699585.2_CLIT1_genomic.fna/target_genomes_gtdb.txt --output GCF_000699585.2_CLIT1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:01,573] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:01,581] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:01,581] [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_900141635.1	s__Peptoclostridium litorale	99.9637	1040	1122	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptoclostridium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000597865.1	s__Peptoclostridium_A acidaminophilum	78.9382	170	1122	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009881055.1	s__Peptoclostridium_A sp009881055	78.2633	132	1122	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:01,583] [INFO] GTDB search result was written to GCF_000699585.2_CLIT1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:01,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:01,586] [INFO] DFAST_QC result json was written to GCF_000699585.2_CLIT1_genomic.fna/dqc_result.json
[2024-01-24 13:58:01,586] [INFO] DFAST_QC completed!
[2024-01-24 13:58:01,586] [INFO] Total running time: 0h1m1s