[2024-01-24 13:28:26,033] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:26,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:26,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference
[2024-01-24 13:28:27,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,384] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg48aeaf09-a6c9-4f16-8889-f478abb254d1/GCF_014651435.1_ASM1465143v1_genomic.fna.gz | prodigal -d GCF_014651435.1_ASM1465143v1_genomic.fna/cds.fna -a GCF_014651435.1_ASM1465143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:45,979] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:45,979] [INFO] Task started: HMMsearch
[2024-01-24 13:28:45,980] [INFO] Running command: hmmsearch --tblout GCF_014651435.1_ASM1465143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference/reference_markers.hmm GCF_014651435.1_ASM1465143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:46,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:46,390] [INFO] Found 6/6 markers.
[2024-01-24 13:28:46,438] [INFO] Query marker FASTA was written to GCF_014651435.1_ASM1465143v1_genomic.fna/markers.fasta
[2024-01-24 13:28:46,439] [INFO] Task started: Blastn
[2024-01-24 13:28:46,439] [INFO] Running command: blastn -query GCF_014651435.1_ASM1465143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference/reference_markers.fasta -out GCF_014651435.1_ASM1465143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:47,420] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:47,424] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:47,424] [INFO] Target genome list was writen to GCF_014651435.1_ASM1465143v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:47,437] [INFO] Task started: fastANI
[2024-01-24 13:28:47,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg48aeaf09-a6c9-4f16-8889-f478abb254d1/GCF_014651435.1_ASM1465143v1_genomic.fna.gz --refList GCF_014651435.1_ASM1465143v1_genomic.fna/target_genomes.txt --output GCF_014651435.1_ASM1465143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:06,847] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:06,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:06,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:06,859] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:06,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:06,860] [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
Pseudoduganella plicata	strain=KCTC 12344	GCA_014651435.1	321984	321984	type	True	100.0	1932	1934	95	conclusive
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	99.9908	1931	1934	95	conclusive
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	86.4204	1558	1934	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	85.6073	1474	1934	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	85.5093	1523	1934	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	83.7462	1398	1934	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	83.4924	1278	1934	95	below_threshold
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	83.2556	1281	1934	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	83.1785	1271	1934	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	80.5187	945	1934	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.5034	762	1934	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	80.2755	940	1934	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	80.1467	880	1934	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.1281	805	1934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,868] [INFO] DFAST Taxonomy check result was written to GCF_014651435.1_ASM1465143v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:06,868] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:06,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:06,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference/checkm_data
[2024-01-24 13:29:06,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:06,928] [INFO] Task started: CheckM
[2024-01-24 13:29:06,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651435.1_ASM1465143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651435.1_ASM1465143v1_genomic.fna/checkm_input GCF_014651435.1_ASM1465143v1_genomic.fna/checkm_result
[2024-01-24 13:30:02,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:02,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:02,840] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:02,840] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:02,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651435.1_ASM1465143v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:02,841] [INFO] Task started: Blastn
[2024-01-24 13:30:02,842] [INFO] Running command: blastn -query GCF_014651435.1_ASM1465143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df29d35-e271-4d92-b509-c76d6d1c851f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651435.1_ASM1465143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:04,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:04,936] [INFO] Selected 8 target genomes.
[2024-01-24 13:30:04,936] [INFO] Target genome list was writen to GCF_014651435.1_ASM1465143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:04,943] [INFO] Task started: fastANI
[2024-01-24 13:30:04,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg48aeaf09-a6c9-4f16-8889-f478abb254d1/GCF_014651435.1_ASM1465143v1_genomic.fna.gz --refList GCF_014651435.1_ASM1465143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651435.1_ASM1465143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:18,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:18,140] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:18,141] [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_004421005.1	s__Pseudoduganella plicata	99.9908	1931	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_008011715.1	s__Pseudoduganella haloabium	86.4473	1528	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_003028855.1	s__Pseudoduganella armeniaca	86.4396	1555	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720835.1	s__Pseudoduganella buxea	85.5936	1476	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002454505.1	s__Pseudoduganella sp002454505	83.9437	1192	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830495.1	s__Pseudoduganella flava	83.7871	1393	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009727155.1	s__Pseudoduganella dura	83.2455	1281	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	82.7333	1314	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:18,144] [INFO] GTDB search result was written to GCF_014651435.1_ASM1465143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:18,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:18,151] [INFO] DFAST_QC result json was written to GCF_014651435.1_ASM1465143v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:18,151] [INFO] DFAST_QC completed!
[2024-01-24 13:30:18,151] [INFO] Total running time: 0h1m52s