[2024-01-25 18:45:50,518] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:50,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:50,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference
[2024-01-25 18:45:51,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:51,675] [INFO] Task started: Prodigal
[2024-01-25 18:45:51,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgfadc6065-1d10-4a64-a3a0-aabe29c1469c/GCF_000307165.1_ASM30716v1_genomic.fna.gz | prodigal -d GCF_000307165.1_ASM30716v1_genomic.fna/cds.fna -a GCF_000307165.1_ASM30716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:55,850] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:55,850] [INFO] Task started: HMMsearch
[2024-01-25 18:45:55,850] [INFO] Running command: hmmsearch --tblout GCF_000307165.1_ASM30716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference/reference_markers.hmm GCF_000307165.1_ASM30716v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:56,065] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:56,068] [INFO] Found 6/6 markers.
[2024-01-25 18:45:56,090] [INFO] Query marker FASTA was written to GCF_000307165.1_ASM30716v1_genomic.fna/markers.fasta
[2024-01-25 18:45:56,090] [INFO] Task started: Blastn
[2024-01-25 18:45:56,090] [INFO] Running command: blastn -query GCF_000307165.1_ASM30716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference/reference_markers.fasta -out GCF_000307165.1_ASM30716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:56,634] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:56,638] [INFO] Selected 24 target genomes.
[2024-01-25 18:45:56,638] [INFO] Target genome list was writen to GCF_000307165.1_ASM30716v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:56,660] [INFO] Task started: fastANI
[2024-01-25 18:45:56,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgfadc6065-1d10-4a64-a3a0-aabe29c1469c/GCF_000307165.1_ASM30716v1_genomic.fna.gz --refList GCF_000307165.1_ASM30716v1_genomic.fna/target_genomes.txt --output GCF_000307165.1_ASM30716v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:10,458] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:10,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:10,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:10,466] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:10,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:10,466] [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
Amphibacillus xylanus	strain=NBRC 15112	GCA_000307165.1	1449	1449	type	True	100.0	856	856	95	conclusive
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	78.8149	74	856	95	below_threshold
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	78.1422	51	856	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	77.3947	89	856	95	below_threshold
Amphibacillus jilinensis	strain=Y1	GCA_000306965.1	1216008	1216008	type	True	77.3763	116	856	95	below_threshold
Pelagirhabdus alkalitolerans	strain=S5	GCA_900096905.1	1612202	1612202	type	True	77.3023	86	856	95	below_threshold
Amphibacillus cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	77.0471	113	856	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.0441	62	856	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	76.8407	73	856	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	76.6941	55	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:10,467] [INFO] DFAST Taxonomy check result was written to GCF_000307165.1_ASM30716v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:10,468] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:10,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:10,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference/checkm_data
[2024-01-25 18:46:10,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:10,496] [INFO] Task started: CheckM
[2024-01-25 18:46:10,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000307165.1_ASM30716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000307165.1_ASM30716v1_genomic.fna/checkm_input GCF_000307165.1_ASM30716v1_genomic.fna/checkm_result
[2024-01-25 18:46:28,855] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:28,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:28,876] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:28,876] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:28,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000307165.1_ASM30716v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:28,876] [INFO] Task started: Blastn
[2024-01-25 18:46:28,877] [INFO] Running command: blastn -query GCF_000307165.1_ASM30716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d33758-c0b6-4b5f-88d9-79149c972f2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000307165.1_ASM30716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:29,604] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:29,609] [INFO] Selected 20 target genomes.
[2024-01-25 18:46:29,609] [INFO] Target genome list was writen to GCF_000307165.1_ASM30716v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:29,624] [INFO] Task started: fastANI
[2024-01-25 18:46:29,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgfadc6065-1d10-4a64-a3a0-aabe29c1469c/GCF_000307165.1_ASM30716v1_genomic.fna.gz --refList GCF_000307165.1_ASM30716v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000307165.1_ASM30716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:41,469] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:41,477] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:41,477] [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_000307165.1	s__Amphibacillus xylanus	100.0	856	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	97.98	97.98	0.94	0.94	2	conclusive
GCA_012838505.1	s__Amphibacillus sp012838505	80.0778	346	856	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_003268595.1	s__Paraliobacillus_A zengyii	78.982	75	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_018919165.1	s__Amphibacillus sp018919165	78.0722	198	856	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_900110345.1	s__Amphibacillus_D marinus	77.4069	90	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.3883	70	856	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_000306965.1	s__Amphibacillus_C jilinensis	77.3549	117	856	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_900096905.1	s__Pelagirhabdus alkalitolerans	77.3065	85	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pelagirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908375.1	s__Amphibacillus_C cookii	77.0709	112	856	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_014083865.1	s__Paraliobacillus salinarum	76.7875	71	856	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_900129485.1	s__Ornithinibacillus halophilus	76.694	55	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:41,478] [INFO] GTDB search result was written to GCF_000307165.1_ASM30716v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:41,479] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:41,482] [INFO] DFAST_QC result json was written to GCF_000307165.1_ASM30716v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:41,483] [INFO] DFAST_QC completed!
[2024-01-25 18:46:41,483] [INFO] Total running time: 0h0m51s