[2024-01-25 19:35:51,299] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,303] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference
[2024-01-25 19:35:52,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,501] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,501] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0f31616-32c7-492e-9d00-3a800c00104b/GCF_030345335.1_ASM3034533v1_genomic.fna.gz | prodigal -d GCF_030345335.1_ASM3034533v1_genomic.fna/cds.fna -a GCF_030345335.1_ASM3034533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:59,882] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:59,883] [INFO] Task started: HMMsearch
[2024-01-25 19:35:59,883] [INFO] Running command: hmmsearch --tblout GCF_030345335.1_ASM3034533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference/reference_markers.hmm GCF_030345335.1_ASM3034533v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:00,236] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:00,237] [INFO] Found 6/6 markers.
[2024-01-25 19:36:00,273] [INFO] Query marker FASTA was written to GCF_030345335.1_ASM3034533v1_genomic.fna/markers.fasta
[2024-01-25 19:36:00,273] [INFO] Task started: Blastn
[2024-01-25 19:36:00,273] [INFO] Running command: blastn -query GCF_030345335.1_ASM3034533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference/reference_markers.fasta -out GCF_030345335.1_ASM3034533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:00,872] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:00,875] [INFO] Selected 38 target genomes.
[2024-01-25 19:36:00,875] [INFO] Target genome list was writen to GCF_030345335.1_ASM3034533v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:00,902] [INFO] Task started: fastANI
[2024-01-25 19:36:00,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0f31616-32c7-492e-9d00-3a800c00104b/GCF_030345335.1_ASM3034533v1_genomic.fna.gz --refList GCF_030345335.1_ASM3034533v1_genomic.fna/target_genomes.txt --output GCF_030345335.1_ASM3034533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:24,690] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:24,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:24,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:24,701] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:36:24,701] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:36:24,701] [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
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	79.7294	420	1265	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	79.7133	423	1265	95	below_threshold
Halobacillus alkaliphilus	strain=FP5	GCA_900113125.1	396056	396056	type	True	78.6383	188	1265	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	78.2706	205	1265	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	78.2447	254	1265	95	below_threshold
Halobacillus ihumii	strain=Marseille-Q1234	GCA_902726645.1	2686092	2686092	type	True	78.0494	196	1265	95	below_threshold
Thalassobacillus pellis	strain=DSM 22784	GCA_016908295.1	748008	748008	type	True	77.9715	91	1265	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	77.8234	157	1265	95	below_threshold
Halobacillus salinus	strain=HSL-3	GCA_004684905.1	192814	192814	type	True	77.8102	146	1265	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	77.6505	200	1265	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	77.6283	174	1265	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	77.6268	123	1265	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	77.2129	50	1265	95	below_threshold
Salimicrobium halophilum	strain=DSM 4771	GCA_900100295.1	86666	86666	type	True	77.1563	72	1265	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.0211	52	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:24,702] [INFO] DFAST Taxonomy check result was written to GCF_030345335.1_ASM3034533v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:24,703] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:24,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:24,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference/checkm_data
[2024-01-25 19:36:24,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:24,741] [INFO] Task started: CheckM
[2024-01-25 19:36:24,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030345335.1_ASM3034533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030345335.1_ASM3034533v1_genomic.fna/checkm_input GCF_030345335.1_ASM3034533v1_genomic.fna/checkm_result
[2024-01-25 19:36:51,186] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:51,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:51,206] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:51,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:51,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030345335.1_ASM3034533v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:51,207] [INFO] Task started: Blastn
[2024-01-25 19:36:51,207] [INFO] Running command: blastn -query GCF_030345335.1_ASM3034533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4b475c2-0494-40a4-a940-dc517c480242/dqc_reference/reference_markers_gtdb.fasta -out GCF_030345335.1_ASM3034533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:51,983] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:51,987] [INFO] Selected 37 target genomes.
[2024-01-25 19:36:51,987] [INFO] Target genome list was writen to GCF_030345335.1_ASM3034533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:52,044] [INFO] Task started: fastANI
[2024-01-25 19:36:52,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0f31616-32c7-492e-9d00-3a800c00104b/GCF_030345335.1_ASM3034533v1_genomic.fna.gz --refList GCF_030345335.1_ASM3034533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030345335.1_ASM3034533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:21,477] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:21,489] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:37:21,490] [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_014636475.1	s__Halobacillus_A andaensis	79.7343	424	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240285.1	s__Halobacillus_A sp900240285	78.825	347	1265	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_902809865.1	s__Halobacillus_A sp902809865	78.749	306	1265	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_004101865.1	s__Halobacillus litoralis_A	78.5896	165	1265	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_016908235.1	s__Halobacillus_A seohaensis	78.4643	366	1265	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_900166655.1	s__Halobacillus_A hunanensis	78.2852	179	1265	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_900166625.1	s__Halobacillus_A massiliensis	78.2146	256	1265	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_902726645.1	s__Halobacillus_A ihumii	78.0596	193	1265	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_016908295.1	s__Thalassobacillus pellis	77.9609	92	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856445.1	s__Halobacillus litoralis	77.8594	166	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCA_004078665.1	s__Halobacillus sp004078665	77.8221	151	1265	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_015905325.1	s__Halobacillus sp015905325	77.7944	136	1265	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_004684905.1	s__Halobacillus salinus	77.7864	144	1265	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_002097535.1	s__Halobacillus mangrovi	77.7748	172	1265	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_007991335.1	s__Halobacillus faecis	77.6682	174	1265	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_000425705.1	s__Halobacillus kuroshimensis	77.6552	124	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.79	98.79	0.92	0.92	2	-
GCF_900104185.1	s__Halobacillus aidingensis	77.6521	202	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	96.52	96.52	0.91	0.91	2	-
GCF_009856415.1	s__Halobacillus litoralis_C	77.6509	187	1265	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_013694105.1	s__Halobacillus locisalis	77.6035	162	1265	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_009858175.1	s__Pontibacillus sp009858175	77.0097	67	1265	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_009650095.1	s__Gracilibacillus sp002797295	76.9779	53	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:21,491] [INFO] GTDB search result was written to GCF_030345335.1_ASM3034533v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:21,492] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:21,496] [INFO] DFAST_QC result json was written to GCF_030345335.1_ASM3034533v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:21,496] [INFO] DFAST_QC completed!
[2024-01-25 19:37:21,496] [INFO] Total running time: 0h1m30s