[2024-01-24 13:46:42,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:43,000] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:43,000] [INFO] DQC Reference Directory: /var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference
[2024-01-24 13:46:44,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:44,388] [INFO] Task started: Prodigal
[2024-01-24 13:46:44,388] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfa2a0f5-959e-418e-85d8-1d6d5b07aafd/GCF_000334155.1_L1_genomic.fna.gz | prodigal -d GCF_000334155.1_L1_genomic.fna/cds.fna -a GCF_000334155.1_L1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:52,943] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:52,944] [INFO] Task started: HMMsearch
[2024-01-24 13:46:52,944] [INFO] Running command: hmmsearch --tblout GCF_000334155.1_L1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference/reference_markers.hmm GCF_000334155.1_L1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:53,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:53,244] [INFO] Found 6/6 markers.
[2024-01-24 13:46:53,282] [INFO] Query marker FASTA was written to GCF_000334155.1_L1_genomic.fna/markers.fasta
[2024-01-24 13:46:53,282] [INFO] Task started: Blastn
[2024-01-24 13:46:53,282] [INFO] Running command: blastn -query GCF_000334155.1_L1_genomic.fna/markers.fasta -db /var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference/reference_markers.fasta -out GCF_000334155.1_L1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:53,909] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:53,913] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:53,913] [INFO] Target genome list was writen to GCF_000334155.1_L1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:53,940] [INFO] Task started: fastANI
[2024-01-24 13:46:53,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa2a0f5-959e-418e-85d8-1d6d5b07aafd/GCF_000334155.1_L1_genomic.fna.gz --refList GCF_000334155.1_L1_genomic.fna/target_genomes.txt --output GCF_000334155.1_L1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:09,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:09,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:09,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:09,250] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:09,250] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:09,250] [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
Halalkalibacterium ligniniphilum	strain=L1	GCA_000334155.1	1134413	1134413	type	True	100.0	1178	1186	95	conclusive
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.182	157	1186	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.3474	132	1186	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	77.3227	134	1186	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	77.3118	130	1186	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	77.1677	82	1186	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	77.1574	95	1186	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.1101	130	1186	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	77.0892	125	1186	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	76.7576	89	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,252] [INFO] DFAST Taxonomy check result was written to GCF_000334155.1_L1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:09,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:09,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:09,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference/checkm_data
[2024-01-24 13:47:09,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:09,293] [INFO] Task started: CheckM
[2024-01-24 13:47:09,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000334155.1_L1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000334155.1_L1_genomic.fna/checkm_input GCF_000334155.1_L1_genomic.fna/checkm_result
[2024-01-24 13:47:39,887] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:39,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:39,915] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:39,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:39,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000334155.1_L1_genomic.fna/markers.fasta)
[2024-01-24 13:47:39,916] [INFO] Task started: Blastn
[2024-01-24 13:47:39,917] [INFO] Running command: blastn -query GCF_000334155.1_L1_genomic.fna/markers.fasta -db /var/lib/cwl/stge64f9df6-2777-42d1-a359-ab5f4b40df73/dqc_reference/reference_markers_gtdb.fasta -out GCF_000334155.1_L1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:40,689] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:40,694] [INFO] Selected 23 target genomes.
[2024-01-24 13:47:40,694] [INFO] Target genome list was writen to GCF_000334155.1_L1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:40,723] [INFO] Task started: fastANI
[2024-01-24 13:47:40,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa2a0f5-959e-418e-85d8-1d6d5b07aafd/GCF_000334155.1_L1_genomic.fna.gz --refList GCF_000334155.1_L1_genomic.fna/target_genomes_gtdb.txt --output GCF_000334155.1_L1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:56,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:56,282] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:56,282] [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_000334155.1	s__Bacillus_AN ligniniphilus	100.0	1178	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_AN	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.174	159	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	77.5041	144	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797395.1	s__45385 sp002797395	77.4051	112	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	77.3685	131	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_000513095.1	s__Bacillus_L wakoensis	77.3433	133	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002109385.1	s__Bacillus_L krulwichiae	77.327	127	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	77.1383	83	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002797325.1	s__Bacillus_S sp002797325	77.1377	113	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590785.1	s__Alkalihalobacillus trypoxylicola	77.131	97	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	98.48	96.97	0.95	0.90	3	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	77.0897	84	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	77.0892	125	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_003318295.1	s__Maribacillus taeanensis	76.7251	59	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:56,284] [INFO] GTDB search result was written to GCF_000334155.1_L1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:56,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:56,287] [INFO] DFAST_QC result json was written to GCF_000334155.1_L1_genomic.fna/dqc_result.json
[2024-01-24 13:47:56,287] [INFO] DFAST_QC completed!
[2024-01-24 13:47:56,287] [INFO] Total running time: 0h1m13s