[2024-01-24 11:51:24,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference
[2024-01-24 11:51:26,299] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,300] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg3df47138-1427-45a5-88da-3c4bd01b5e0b/GCF_007991355.1_ASM799135v1_genomic.fna.gz | prodigal -d GCF_007991355.1_ASM799135v1_genomic.fna/cds.fna -a GCF_007991355.1_ASM799135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:31,608] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:31,608] [INFO] Task started: HMMsearch
[2024-01-24 11:51:31,608] [INFO] Running command: hmmsearch --tblout GCF_007991355.1_ASM799135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference/reference_markers.hmm GCF_007991355.1_ASM799135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:31,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:31,852] [INFO] Found 6/6 markers.
[2024-01-24 11:51:31,882] [INFO] Query marker FASTA was written to GCF_007991355.1_ASM799135v1_genomic.fna/markers.fasta
[2024-01-24 11:51:31,882] [INFO] Task started: Blastn
[2024-01-24 11:51:31,882] [INFO] Running command: blastn -query GCF_007991355.1_ASM799135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference/reference_markers.fasta -out GCF_007991355.1_ASM799135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:32,465] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:32,469] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:32,469] [INFO] Target genome list was writen to GCF_007991355.1_ASM799135v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:32,490] [INFO] Task started: fastANI
[2024-01-24 11:51:32,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg3df47138-1427-45a5-88da-3c4bd01b5e0b/GCF_007991355.1_ASM799135v1_genomic.fna.gz --refList GCF_007991355.1_ASM799135v1_genomic.fna/target_genomes.txt --output GCF_007991355.1_ASM799135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:40,198] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:40,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:40,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:40,207] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:51:40,207] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:40,208] [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
Halolactibacillus alkaliphilus	strain=NBRC 103919	GCA_007991355.1	442899	442899	type	True	100.0	900	905	95	conclusive
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_014645215.1	442899	442899	type	True	99.9966	903	905	95	conclusive
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_900115465.1	442899	442899	type	True	99.9965	903	905	95	conclusive
Halolactibacillus miurensis	strain=NBRC 100873	GCA_007990305.1	306541	306541	type	True	81.5765	492	905	95	below_threshold
Halolactibacillus miurensis	strain=DSM 17074	GCA_900116255.1	306541	306541	type	True	81.5077	508	905	95	below_threshold
Halolactibacillus halophilus	strain=DSM 17073	GCA_900115605.1	306540	306540	type	True	80.8109	388	905	95	below_threshold
Halolactibacillus halophilus	strain=NBRC 100868	GCA_007990285.1	306540	306540	type	True	80.6347	382	905	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.984	68	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:40,209] [INFO] DFAST Taxonomy check result was written to GCF_007991355.1_ASM799135v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:40,210] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:40,210] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:40,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference/checkm_data
[2024-01-24 11:51:40,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:40,245] [INFO] Task started: CheckM
[2024-01-24 11:51:40,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991355.1_ASM799135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991355.1_ASM799135v1_genomic.fna/checkm_input GCF_007991355.1_ASM799135v1_genomic.fna/checkm_result
[2024-01-24 11:52:03,437] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:03,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:03,462] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:03,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:03,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991355.1_ASM799135v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:03,463] [INFO] Task started: Blastn
[2024-01-24 11:52:03,464] [INFO] Running command: blastn -query GCF_007991355.1_ASM799135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ef0bdb0-8363-45ab-8c55-0c34d59df5dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991355.1_ASM799135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:04,290] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:04,294] [INFO] Selected 18 target genomes.
[2024-01-24 11:52:04,294] [INFO] Target genome list was writen to GCF_007991355.1_ASM799135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:04,308] [INFO] Task started: fastANI
[2024-01-24 11:52:04,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg3df47138-1427-45a5-88da-3c4bd01b5e0b/GCF_007991355.1_ASM799135v1_genomic.fna.gz --refList GCF_007991355.1_ASM799135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991355.1_ASM799135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:15,975] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:15,988] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:15,989] [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_900115465.1	s__Halolactibacillus alkaliphilus	99.9965	903	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	conclusive
GCF_900116255.1	s__Halolactibacillus miurensis	81.519	509	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	-
GCF_900115605.1	s__Halolactibacillus halophilus	80.7881	389	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003201605.1	s__Streptohalobacillus salinus	78.5785	186	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Streptohalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.984	68	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_018919165.1	s__Amphibacillus sp018919165	77.5477	73	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	77.4974	113	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.433	82	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908375.1	s__Amphibacillus_C cookii	77.2795	117	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,990] [INFO] GTDB search result was written to GCF_007991355.1_ASM799135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:15,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:15,995] [INFO] DFAST_QC result json was written to GCF_007991355.1_ASM799135v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:15,996] [INFO] DFAST_QC completed!
[2024-01-24 11:52:15,996] [INFO] Total running time: 0h0m51s