[2023-06-17 14:26:39,932] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:26:39,952] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:26:39,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference
[2023-06-17 14:26:42,200] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:26:42,201] [INFO] Task started: Prodigal
[2023-06-17 14:26:42,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ca34f24-fe21-4aff-bdae-55546361197f/GCA_028708575.1_ASM2870857v1_genomic.fna.gz | prodigal -d GCA_028708575.1_ASM2870857v1_genomic.fna/cds.fna -a GCA_028708575.1_ASM2870857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:26:45,254] [INFO] Task succeeded: Prodigal
[2023-06-17 14:26:45,255] [INFO] Task started: HMMsearch
[2023-06-17 14:26:45,255] [INFO] Running command: hmmsearch --tblout GCA_028708575.1_ASM2870857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference/reference_markers.hmm GCA_028708575.1_ASM2870857v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:26:45,485] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:26:45,487] [INFO] Found 6/6 markers.
[2023-06-17 14:26:45,512] [INFO] Query marker FASTA was written to GCA_028708575.1_ASM2870857v1_genomic.fna/markers.fasta
[2023-06-17 14:26:45,512] [INFO] Task started: Blastn
[2023-06-17 14:26:45,512] [INFO] Running command: blastn -query GCA_028708575.1_ASM2870857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference/reference_markers.fasta -out GCA_028708575.1_ASM2870857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:26:47,239] [INFO] Task succeeded: Blastn
[2023-06-17 14:26:47,244] [INFO] Selected 24 target genomes.
[2023-06-17 14:26:47,245] [INFO] Target genome list was writen to GCA_028708575.1_ASM2870857v1_genomic.fna/target_genomes.txt
[2023-06-17 14:26:47,251] [INFO] Task started: fastANI
[2023-06-17 14:26:47,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca34f24-fe21-4aff-bdae-55546361197f/GCA_028708575.1_ASM2870857v1_genomic.fna.gz --refList GCA_028708575.1_ASM2870857v1_genomic.fna/target_genomes.txt --output GCA_028708575.1_ASM2870857v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:26:59,554] [INFO] Task succeeded: fastANI
[2023-06-17 14:26:59,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:26:59,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:26:59,566] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:26:59,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:26:59,567] [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
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	76.5586	93	613	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	76.154	79	613	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	75.9362	55	613	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	75.8321	55	613	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:26:59,569] [INFO] DFAST Taxonomy check result was written to GCA_028708575.1_ASM2870857v1_genomic.fna/tc_result.tsv
[2023-06-17 14:26:59,570] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:26:59,570] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:26:59,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference/checkm_data
[2023-06-17 14:26:59,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:26:59,600] [INFO] Task started: CheckM
[2023-06-17 14:26:59,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708575.1_ASM2870857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708575.1_ASM2870857v1_genomic.fna/checkm_input GCA_028708575.1_ASM2870857v1_genomic.fna/checkm_result
[2023-06-17 14:27:16,798] [INFO] Task succeeded: CheckM
[2023-06-17 14:27:16,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:27:16,821] [INFO] ===== Completeness check finished =====
[2023-06-17 14:27:16,822] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:27:16,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708575.1_ASM2870857v1_genomic.fna/markers.fasta)
[2023-06-17 14:27:16,823] [INFO] Task started: Blastn
[2023-06-17 14:27:16,823] [INFO] Running command: blastn -query GCA_028708575.1_ASM2870857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c08e88d-29e4-4a52-a4a0-ad62fbc9210a/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708575.1_ASM2870857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:27:17,619] [INFO] Task succeeded: Blastn
[2023-06-17 14:27:17,624] [INFO] Selected 21 target genomes.
[2023-06-17 14:27:17,624] [INFO] Target genome list was writen to GCA_028708575.1_ASM2870857v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:27:17,643] [INFO] Task started: fastANI
[2023-06-17 14:27:17,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca34f24-fe21-4aff-bdae-55546361197f/GCA_028708575.1_ASM2870857v1_genomic.fna.gz --refList GCA_028708575.1_ASM2870857v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708575.1_ASM2870857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:27:26,639] [INFO] Task succeeded: fastANI
[2023-06-17 14:27:26,653] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:27:26,654] [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_012520755.1	s__UBA3583 sp012520755	82.5377	365	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__UBA3583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375815.1	s__UBA3583 sp002375815	77.4555	179	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__UBA3583	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005046945.1	s__Tissierella_B creatinini	77.1867	82	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385225.1	s__JACRTK01 sp014385225	76.7568	64	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JACRTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695605.1	s__DSM105185 sp009695605	76.5586	93	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
GCF_902386935.1	s__CABMKH01 sp902386935	76.2778	57	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__CABMKH01	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018917865.1	s__MSJ-40 sp018917865	76.1733	78	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__MSJ-40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016767175.1	s__Keratinibaculum paraultunense	75.9362	55	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-17 14:27:26,656] [INFO] GTDB search result was written to GCA_028708575.1_ASM2870857v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:27:26,657] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:27:26,662] [INFO] DFAST_QC result json was written to GCA_028708575.1_ASM2870857v1_genomic.fna/dqc_result.json
[2023-06-17 14:27:26,662] [INFO] DFAST_QC completed!
[2023-06-17 14:27:26,662] [INFO] Total running time: 0h0m47s