[2024-01-24 13:01:12,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference
[2024-01-24 13:01:13,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,744] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cf4e84d-a3f7-42ab-94ad-1a5f9fe0ad41/GCF_000425205.1_ASM42520v1_genomic.fna.gz | prodigal -d GCF_000425205.1_ASM42520v1_genomic.fna/cds.fna -a GCF_000425205.1_ASM42520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:22,391] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:22,392] [INFO] Task started: HMMsearch
[2024-01-24 13:01:22,392] [INFO] Running command: hmmsearch --tblout GCF_000425205.1_ASM42520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference/reference_markers.hmm GCF_000425205.1_ASM42520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:22,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:22,769] [INFO] Found 6/6 markers.
[2024-01-24 13:01:22,813] [INFO] Query marker FASTA was written to GCF_000425205.1_ASM42520v1_genomic.fna/markers.fasta
[2024-01-24 13:01:22,813] [INFO] Task started: Blastn
[2024-01-24 13:01:22,814] [INFO] Running command: blastn -query GCF_000425205.1_ASM42520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference/reference_markers.fasta -out GCF_000425205.1_ASM42520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:23,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:23,439] [INFO] Selected 23 target genomes.
[2024-01-24 13:01:23,439] [INFO] Target genome list was writen to GCF_000425205.1_ASM42520v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:23,448] [INFO] Task started: fastANI
[2024-01-24 13:01:23,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf4e84d-a3f7-42ab-94ad-1a5f9fe0ad41/GCF_000425205.1_ASM42520v1_genomic.fna.gz --refList GCF_000425205.1_ASM42520v1_genomic.fna/target_genomes.txt --output GCF_000425205.1_ASM42520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:38,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:38,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:38,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:38,210] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:38,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:38,210] [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
Pontibacillus halophilus	strain=DSM 19796	GCA_000425205.1	516704	516704	type	True	100.0	1204	1205	95	conclusive
Pontibacillus halophilus	strain=JSM 076056	GCA_000775595.1	516704	516704	type	True	99.9769	1142	1205	95	conclusive
Halobacillus salinus	strain=HSL-3	GCA_004684905.1	192814	192814	type	True	77.7755	64	1205	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	77.63	58	1205	95	below_threshold
Pontibacillus marinus	strain=BH030004	GCA_000775605.1	273164	273164	type	True	77.3967	107	1205	95	below_threshold
Pontibacillus marinus	strain=DSM 16465	GCA_000425225.1	273164	273164	type	True	77.3462	115	1205	95	below_threshold
Pontibacillus yanchengensis	strain=Y32	GCA_000770635.1	462910	462910	type	True	77.2846	115	1205	95	below_threshold
Pontibacillus litoralis	strain=JSM 072002	GCA_000775615.1	516703	516703	type	True	77.2685	84	1205	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	77.1316	59	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:38,212] [INFO] DFAST Taxonomy check result was written to GCF_000425205.1_ASM42520v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:38,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:38,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:38,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference/checkm_data
[2024-01-24 13:01:38,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:38,252] [INFO] Task started: CheckM
[2024-01-24 13:01:38,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425205.1_ASM42520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425205.1_ASM42520v1_genomic.fna/checkm_input GCF_000425205.1_ASM42520v1_genomic.fna/checkm_result
[2024-01-24 13:02:09,318] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:09,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:09,343] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:09,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:09,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425205.1_ASM42520v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:09,344] [INFO] Task started: Blastn
[2024-01-24 13:02:09,344] [INFO] Running command: blastn -query GCF_000425205.1_ASM42520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff96e05-bd5b-42ed-950f-60242d42685c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425205.1_ASM42520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:10,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:10,112] [INFO] Selected 29 target genomes.
[2024-01-24 13:02:10,112] [INFO] Target genome list was writen to GCF_000425205.1_ASM42520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:10,134] [INFO] Task started: fastANI
[2024-01-24 13:02:10,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf4e84d-a3f7-42ab-94ad-1a5f9fe0ad41/GCF_000425205.1_ASM42520v1_genomic.fna.gz --refList GCF_000425205.1_ASM42520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425205.1_ASM42520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:28,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:28,076] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:28,076] [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_000425205.1	s__Pontibacillus_A halophilus	100.0	1204	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004684905.1	s__Halobacillus salinus	77.7755	64	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.08	98.08	0.93	0.93	2	-
GCF_009856445.1	s__Halobacillus litoralis	77.634	58	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCF_009856295.1	s__Pontibacillus yanchengensis_A	77.4334	117	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	99.50	99.50	0.96	0.96	2	-
GCF_000425225.1	s__Pontibacillus marinus	77.4179	115	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902809865.1	s__Halobacillus_A sp902809865	77.367	57	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770635.1	s__Pontibacillus yanchengensis	77.2846	115	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002097535.1	s__Halobacillus mangrovi	77.2204	58	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775615.1	s__Pontibacillus litoralis	77.2176	84	1205	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:28,078] [INFO] GTDB search result was written to GCF_000425205.1_ASM42520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:28,079] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:28,082] [INFO] DFAST_QC result json was written to GCF_000425205.1_ASM42520v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:28,082] [INFO] DFAST_QC completed!
[2024-01-24 13:02:28,082] [INFO] Total running time: 0h1m16s