[2023-06-17 06:26:14,669] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:26:14,673] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:26:14,673] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference
[2023-06-17 06:26:16,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:26:16,085] [INFO] Task started: Prodigal
[2023-06-17 06:26:16,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dde58b6-5445-4d2b-b9cc-5b97165d2b37/GCA_028709205.1_ASM2870920v1_genomic.fna.gz | prodigal -d GCA_028709205.1_ASM2870920v1_genomic.fna/cds.fna -a GCA_028709205.1_ASM2870920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:26:24,428] [INFO] Task succeeded: Prodigal
[2023-06-17 06:26:24,428] [INFO] Task started: HMMsearch
[2023-06-17 06:26:24,429] [INFO] Running command: hmmsearch --tblout GCA_028709205.1_ASM2870920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference/reference_markers.hmm GCA_028709205.1_ASM2870920v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:26:24,725] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:26:24,726] [INFO] Found 6/6 markers.
[2023-06-17 06:26:24,753] [INFO] Query marker FASTA was written to GCA_028709205.1_ASM2870920v1_genomic.fna/markers.fasta
[2023-06-17 06:26:24,754] [INFO] Task started: Blastn
[2023-06-17 06:26:24,754] [INFO] Running command: blastn -query GCA_028709205.1_ASM2870920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference/reference_markers.fasta -out GCA_028709205.1_ASM2870920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:26:25,374] [INFO] Task succeeded: Blastn
[2023-06-17 06:26:25,398] [INFO] Selected 22 target genomes.
[2023-06-17 06:26:25,398] [INFO] Target genome list was writen to GCA_028709205.1_ASM2870920v1_genomic.fna/target_genomes.txt
[2023-06-17 06:26:25,419] [INFO] Task started: fastANI
[2023-06-17 06:26:25,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dde58b6-5445-4d2b-b9cc-5b97165d2b37/GCA_028709205.1_ASM2870920v1_genomic.fna.gz --refList GCA_028709205.1_ASM2870920v1_genomic.fna/target_genomes.txt --output GCA_028709205.1_ASM2870920v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:26:45,865] [INFO] Task succeeded: fastANI
[2023-06-17 06:26:45,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:26:45,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:26:45,871] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 06:26:45,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 06:26:45,872] [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	99.5193	688	700	95	conclusive
Proteiniphilum acetatigenes	strain=DSM 18083	GCA_000380985.1	294710	294710	type	True	77.0964	73	700	95	below_threshold
Proteiniphilum saccharofermentans	strain=M3/6	GCA_900095135.1	1642647	1642647	type	True	76.4371	79	700	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:26:45,874] [INFO] DFAST Taxonomy check result was written to GCA_028709205.1_ASM2870920v1_genomic.fna/tc_result.tsv
[2023-06-17 06:26:45,883] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:26:45,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:26:45,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference/checkm_data
[2023-06-17 06:26:45,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:26:45,919] [INFO] Task started: CheckM
[2023-06-17 06:26:45,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028709205.1_ASM2870920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028709205.1_ASM2870920v1_genomic.fna/checkm_input GCA_028709205.1_ASM2870920v1_genomic.fna/checkm_result
[2023-06-17 06:27:15,723] [INFO] Task succeeded: CheckM
[2023-06-17 06:27:15,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:27:15,747] [INFO] ===== Completeness check finished =====
[2023-06-17 06:27:15,747] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:27:15,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028709205.1_ASM2870920v1_genomic.fna/markers.fasta)
[2023-06-17 06:27:15,748] [INFO] Task started: Blastn
[2023-06-17 06:27:15,748] [INFO] Running command: blastn -query GCA_028709205.1_ASM2870920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5c30ca-f5d4-4f30-a924-9e589aeafbb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_028709205.1_ASM2870920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:27:16,581] [INFO] Task succeeded: Blastn
[2023-06-17 06:27:16,587] [INFO] Selected 24 target genomes.
[2023-06-17 06:27:16,588] [INFO] Target genome list was writen to GCA_028709205.1_ASM2870920v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:27:16,598] [INFO] Task started: fastANI
[2023-06-17 06:27:16,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dde58b6-5445-4d2b-b9cc-5b97165d2b37/GCA_028709205.1_ASM2870920v1_genomic.fna.gz --refList GCA_028709205.1_ASM2870920v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028709205.1_ASM2870920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:27:28,929] [INFO] Task succeeded: fastANI
[2023-06-17 06:27:28,946] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:27:28,947] [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_001282625.1	s__Fermentimonas massiliensis	99.5193	688	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	99.52	99.22	0.95	0.88	9	conclusive
GCA_002398875.1	s__Fermentimonas sp002398875	79.3156	401	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	99.50	99.32	0.87	0.84	9	-
GCA_012841425.1	s__Fermentimonas sp012841425	77.4532	94	700	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	77.4072	185	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305715.1	s__Proteiniphilum sp002305715	77.3498	69	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513315.1	s__Fermentimonas sp012513315	77.2479	130	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Fermentimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408485.1	s__Proteiniphilum sp002408485	77.1673	66	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.68	99.43	0.85	0.77	12	-
GCF_000380985.1	s__Proteiniphilum acetatigenes	77.0906	73	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	98.04	98.04	0.89	0.89	2	-
GCA_002410345.1	s__Proteiniphilum sp002410345	77.0261	88	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.79	99.65	0.86	0.79	18	-
GCA_002398565.1	s__Proteiniphilum sp002398565	76.7408	51	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.17	99.05	0.83	0.81	4	-
GCA_001768325.1	s__Proteiniphilum sp001768325	76.6984	70	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.21	95.58	0.95	0.81	7	-
GCA_012728155.1	s__Proteiniphilum sp012728155	76.672	59	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383605.1	s__Proteiniphilum sp002383605	76.6685	64	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.07	99.07	0.78	0.78	2	-
GCA_002410825.1	s__Proteiniphilum sp002410825	76.517	71	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095135.1	s__Proteiniphilum saccharofermentans	76.4111	80	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	96.87	96.82	0.85	0.85	3	-
GCA_002411515.1	s__Proteiniphilum sp002411515	76.2063	58	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.02	99.02	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-17 06:27:28,949] [INFO] GTDB search result was written to GCA_028709205.1_ASM2870920v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:27:28,949] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:27:28,953] [INFO] DFAST_QC result json was written to GCA_028709205.1_ASM2870920v1_genomic.fna/dqc_result.json
[2023-06-17 06:27:28,953] [INFO] DFAST_QC completed!
[2023-06-17 06:27:28,953] [INFO] Total running time: 0h1m14s