[2023-06-17 15:15:54,518] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:15:54,522] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:15:54,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference
[2023-06-17 15:15:55,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:15:55,754] [INFO] Task started: Prodigal
[2023-06-17 15:15:55,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg9888c716-34bb-48ce-9546-c34933682ee2/GCA_028708495.1_ASM2870849v1_genomic.fna.gz | prodigal -d GCA_028708495.1_ASM2870849v1_genomic.fna/cds.fna -a GCA_028708495.1_ASM2870849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:16:04,681] [INFO] Task succeeded: Prodigal
[2023-06-17 15:16:04,682] [INFO] Task started: HMMsearch
[2023-06-17 15:16:04,682] [INFO] Running command: hmmsearch --tblout GCA_028708495.1_ASM2870849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference/reference_markers.hmm GCA_028708495.1_ASM2870849v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:16:04,890] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:16:04,891] [INFO] Found 6/6 markers.
[2023-06-17 15:16:04,915] [INFO] Query marker FASTA was written to GCA_028708495.1_ASM2870849v1_genomic.fna/markers.fasta
[2023-06-17 15:16:04,915] [INFO] Task started: Blastn
[2023-06-17 15:16:04,915] [INFO] Running command: blastn -query GCA_028708495.1_ASM2870849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference/reference_markers.fasta -out GCA_028708495.1_ASM2870849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:16:05,475] [INFO] Task succeeded: Blastn
[2023-06-17 15:16:05,479] [INFO] Selected 21 target genomes.
[2023-06-17 15:16:05,479] [INFO] Target genome list was writen to GCA_028708495.1_ASM2870849v1_genomic.fna/target_genomes.txt
[2023-06-17 15:16:05,482] [INFO] Task started: fastANI
[2023-06-17 15:16:05,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg9888c716-34bb-48ce-9546-c34933682ee2/GCA_028708495.1_ASM2870849v1_genomic.fna.gz --refList GCA_028708495.1_ASM2870849v1_genomic.fna/target_genomes.txt --output GCA_028708495.1_ASM2870849v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:16:18,178] [INFO] Task succeeded: fastANI
[2023-06-17 15:16:18,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:16:18,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:16:18,184] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 15:16:18,184] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 15:16:18,184] [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
Lascolabacillus massiliensis	strain=SIT8	GCA_001282625.1	1627894	1627894	type	True	79.4181	430	768	95	below_threshold
Proteiniphilum acetatigenes	strain=DSM 18083	GCA_000380985.1	294710	294710	type	True	77.0377	69	768	95	below_threshold
Proteiniphilum saccharofermentans	strain=M3/6	GCA_900095135.1	1642647	1642647	type	True	76.6565	70	768	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 15:16:18,186] [INFO] DFAST Taxonomy check result was written to GCA_028708495.1_ASM2870849v1_genomic.fna/tc_result.tsv
[2023-06-17 15:16:18,187] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:16:18,187] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:16:18,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference/checkm_data
[2023-06-17 15:16:18,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:16:18,214] [INFO] Task started: CheckM
[2023-06-17 15:16:18,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708495.1_ASM2870849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708495.1_ASM2870849v1_genomic.fna/checkm_input GCA_028708495.1_ASM2870849v1_genomic.fna/checkm_result
[2023-06-17 15:16:48,950] [INFO] Task succeeded: CheckM
[2023-06-17 15:16:48,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:16:48,969] [INFO] ===== Completeness check finished =====
[2023-06-17 15:16:48,970] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:16:48,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708495.1_ASM2870849v1_genomic.fna/markers.fasta)
[2023-06-17 15:16:48,970] [INFO] Task started: Blastn
[2023-06-17 15:16:48,970] [INFO] Running command: blastn -query GCA_028708495.1_ASM2870849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg132286c0-fe45-42fa-a9a7-5adb93332a7e/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708495.1_ASM2870849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:16:49,741] [INFO] Task succeeded: Blastn
[2023-06-17 15:16:49,745] [INFO] Selected 22 target genomes.
[2023-06-17 15:16:49,745] [INFO] Target genome list was writen to GCA_028708495.1_ASM2870849v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:16:49,753] [INFO] Task started: fastANI
[2023-06-17 15:16:49,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg9888c716-34bb-48ce-9546-c34933682ee2/GCA_028708495.1_ASM2870849v1_genomic.fna.gz --refList GCA_028708495.1_ASM2870849v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708495.1_ASM2870849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:17:00,673] [INFO] Task succeeded: fastANI
[2023-06-17 15:17:00,686] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:17:00,686] [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_002398875.1	s__Fermentimonas sp002398875	99.5476	717	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	99.50	99.32	0.87	0.84	9	conclusive
GCF_001282625.1	s__Fermentimonas massiliensis	79.4128	431	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	99.52	99.22	0.95	0.88	9	-
GCA_012841425.1	s__Fermentimonas sp012841425	77.8196	83	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478775.1	s__Fermentimonas sp015478775	77.3714	175	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513315.1	s__Fermentimonas sp012513315	77.3387	140	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768325.1	s__Proteiniphilum sp001768325	77.2699	80	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.21	95.58	0.95	0.81	7	-
GCA_002398565.1	s__Proteiniphilum sp002398565	76.9889	72	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.17	99.05	0.83	0.81	4	-
GCA_002383605.1	s__Proteiniphilum sp002383605	76.9012	82	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.07	99.07	0.78	0.78	2	-
GCA_002305715.1	s__Proteiniphilum sp002305715	76.7772	80	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002411515.1	s__Proteiniphilum sp002411515	76.7523	68	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.02	99.02	0.84	0.84	2	-
GCA_002410345.1	s__Proteiniphilum sp002410345	76.7388	81	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.79	99.65	0.86	0.79	18	-
GCA_002410825.1	s__Proteiniphilum sp002410825	76.5665	67	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408485.1	s__Proteiniphilum sp002408485	76.4735	88	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.68	99.43	0.85	0.77	12	-
--------------------------------------------------------------------------------
[2023-06-17 15:17:00,689] [INFO] GTDB search result was written to GCA_028708495.1_ASM2870849v1_genomic.fna/result_gtdb.tsv
[2023-06-17 15:17:00,689] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:17:00,693] [INFO] DFAST_QC result json was written to GCA_028708495.1_ASM2870849v1_genomic.fna/dqc_result.json
[2023-06-17 15:17:00,693] [INFO] DFAST_QC completed!
[2023-06-17 15:17:00,694] [INFO] Total running time: 0h1m6s