[2024-01-24 13:49:45,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference
[2024-01-24 13:49:46,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,934] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg7acd0afd-cf0e-42b6-97f1-5bc81fd1480d/GCF_000511355.1_ASM51135v1_genomic.fna.gz | prodigal -d GCF_000511355.1_ASM51135v1_genomic.fna/cds.fna -a GCF_000511355.1_ASM51135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:02,368] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:02,369] [INFO] Task started: HMMsearch
[2024-01-24 13:50:02,369] [INFO] Running command: hmmsearch --tblout GCF_000511355.1_ASM51135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference/reference_markers.hmm GCF_000511355.1_ASM51135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:02,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:02,653] [INFO] Found 6/6 markers.
[2024-01-24 13:50:02,699] [INFO] Query marker FASTA was written to GCF_000511355.1_ASM51135v1_genomic.fna/markers.fasta
[2024-01-24 13:50:02,700] [INFO] Task started: Blastn
[2024-01-24 13:50:02,700] [INFO] Running command: blastn -query GCF_000511355.1_ASM51135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference/reference_markers.fasta -out GCF_000511355.1_ASM51135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:03,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:03,545] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:03,546] [INFO] Target genome list was writen to GCF_000511355.1_ASM51135v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:03,549] [INFO] Task started: fastANI
[2024-01-24 13:50:03,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg7acd0afd-cf0e-42b6-97f1-5bc81fd1480d/GCF_000511355.1_ASM51135v1_genomic.fna.gz --refList GCF_000511355.1_ASM51135v1_genomic.fna/target_genomes.txt --output GCF_000511355.1_ASM51135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:13,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:13,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:13,917] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:13,917] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:13,917] [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
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	100.0	1547	1549	95	conclusive
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	88.2473	1241	1549	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	85.9383	1153	1549	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	85.9256	1130	1549	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	85.7817	1118	1549	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.7961	639	1549	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.9023	345	1549	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8591	344	1549	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.8204	367	1549	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6851	302	1549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,919] [INFO] DFAST Taxonomy check result was written to GCF_000511355.1_ASM51135v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:13,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:13,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:13,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference/checkm_data
[2024-01-24 13:50:13,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:13,970] [INFO] Task started: CheckM
[2024-01-24 13:50:13,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000511355.1_ASM51135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000511355.1_ASM51135v1_genomic.fna/checkm_input GCF_000511355.1_ASM51135v1_genomic.fna/checkm_result
[2024-01-24 13:50:59,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:59,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:59,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:59,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:59,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000511355.1_ASM51135v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:59,257] [INFO] Task started: Blastn
[2024-01-24 13:50:59,257] [INFO] Running command: blastn -query GCF_000511355.1_ASM51135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83c0bcf-2c8c-4954-b662-fa92974128df/dqc_reference/reference_markers_gtdb.fasta -out GCF_000511355.1_ASM51135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:00,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:00,635] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:00,635] [INFO] Target genome list was writen to GCF_000511355.1_ASM51135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:00,644] [INFO] Task started: fastANI
[2024-01-24 13:51:00,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg7acd0afd-cf0e-42b6-97f1-5bc81fd1480d/GCF_000511355.1_ASM51135v1_genomic.fna.gz --refList GCF_000511355.1_ASM51135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000511355.1_ASM51135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:13,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:13,871] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:13,872] [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_000511355.1	s__Leisingera methylohalidivorans	100.0	1546	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004123675.1	s__Leisingera sp004123675	88.9312	1204	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_000473165.1	s__Leisingera aquimarina	88.2714	1240	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	85.9674	1156	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	85.9148	1132	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000473145.1	s__Leisingera daeponensis	85.7795	1117	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_013317235.1	s__Leisingera sp013317235	85.5167	1138	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	85.5036	1101	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_001679925.1	s__Leisingera sp001679925	85.2108	1109	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	85.0932	1054	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	84.8856	1087	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,874] [INFO] GTDB search result was written to GCF_000511355.1_ASM51135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:13,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:13,878] [INFO] DFAST_QC result json was written to GCF_000511355.1_ASM51135v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:13,878] [INFO] DFAST_QC completed!
[2024-01-24 13:51:13,878] [INFO] Total running time: 0h1m28s