[2024-01-24 14:12:46,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:46,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:46,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference
[2024-01-24 14:12:47,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,939] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg781ccbdb-9829-4910-aa62-ee3626999026/GCF_002287355.1_ASM228735v1_genomic.fna.gz | prodigal -d GCF_002287355.1_ASM228735v1_genomic.fna/cds.fna -a GCF_002287355.1_ASM228735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:57,576] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:57,576] [INFO] Task started: HMMsearch
[2024-01-24 14:12:57,576] [INFO] Running command: hmmsearch --tblout GCF_002287355.1_ASM228735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference/reference_markers.hmm GCF_002287355.1_ASM228735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:57,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:57,852] [INFO] Found 6/6 markers.
[2024-01-24 14:12:57,885] [INFO] Query marker FASTA was written to GCF_002287355.1_ASM228735v1_genomic.fna/markers.fasta
[2024-01-24 14:12:57,886] [INFO] Task started: Blastn
[2024-01-24 14:12:57,886] [INFO] Running command: blastn -query GCF_002287355.1_ASM228735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference/reference_markers.fasta -out GCF_002287355.1_ASM228735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:58,723] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:58,728] [INFO] Selected 16 target genomes.
[2024-01-24 14:12:58,728] [INFO] Target genome list was writen to GCF_002287355.1_ASM228735v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:58,743] [INFO] Task started: fastANI
[2024-01-24 14:12:58,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg781ccbdb-9829-4910-aa62-ee3626999026/GCF_002287355.1_ASM228735v1_genomic.fna.gz --refList GCF_002287355.1_ASM228735v1_genomic.fna/target_genomes.txt --output GCF_002287355.1_ASM228735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:09,161] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:09,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:09,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:09,176] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:09,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:09,176] [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
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	100.0	1050	1060	95	conclusive
Tamilnaduibacter salinus	strain=DSM 28688	GCA_003096655.1	1484056	1484056	type	True	98.7622	989	1060	95	conclusive
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	78.4366	365	1060	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.3653	356	1060	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.0875	357	1060	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	77.7753	219	1060	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	77.7744	215	1060	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	77.7534	255	1060	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	77.6815	219	1060	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	77.6638	271	1060	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	77.2175	207	1060	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	77.0076	191	1060	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.6643	115	1060	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.4664	103	1060	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	76.3367	91	1060	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	75.8597	50	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:09,178] [INFO] DFAST Taxonomy check result was written to GCF_002287355.1_ASM228735v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:09,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:09,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:09,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference/checkm_data
[2024-01-24 14:13:09,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:09,216] [INFO] Task started: CheckM
[2024-01-24 14:13:09,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002287355.1_ASM228735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002287355.1_ASM228735v1_genomic.fna/checkm_input GCF_002287355.1_ASM228735v1_genomic.fna/checkm_result
[2024-01-24 14:13:42,672] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:42,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:42,693] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:42,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:42,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002287355.1_ASM228735v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:42,694] [INFO] Task started: Blastn
[2024-01-24 14:13:42,694] [INFO] Running command: blastn -query GCF_002287355.1_ASM228735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23d63027-7104-4f51-b70e-c30d7641a46b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002287355.1_ASM228735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:44,048] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:44,052] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:44,052] [INFO] Target genome list was writen to GCF_002287355.1_ASM228735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:44,065] [INFO] Task started: fastANI
[2024-01-24 14:13:44,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg781ccbdb-9829-4910-aa62-ee3626999026/GCF_002287355.1_ASM228735v1_genomic.fna.gz --refList GCF_002287355.1_ASM228735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002287355.1_ASM228735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:55,863] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:55,880] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:55,880] [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_003096655.1	s__Tamilnaduibacter salinus	98.7622	989	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Tamilnaduibacter	95.0	98.82	98.82	0.93	0.93	2	conclusive
GCF_003258515.1	s__Marinobacter_A bohaiensis	78.4366	365	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.3545	357	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	78.1633	349	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_003315345.1	s__Marinobacter pelagius_A	77.8485	266	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	77.8019	232	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_900115175.1	s__Marinobacter gudaonensis	77.7646	254	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114155.1	s__Marinobacter persicus	77.7601	216	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002934325.1	s__Marinobacter persicus_A	77.7149	225	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	77.7127	257	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981305.1	s__Marinobacter lutaoensis	77.6853	269	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	77.6718	238	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111555.1	s__Marinobacter segnicrescens	77.6669	220	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	77.6351	217	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359475.1	s__Marinobacter sp014359475	77.6016	209	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	77.2653	172	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008795985.1	s__Marinobacter halotolerans	77.2424	205	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:55,881] [INFO] GTDB search result was written to GCF_002287355.1_ASM228735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:55,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:55,886] [INFO] DFAST_QC result json was written to GCF_002287355.1_ASM228735v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:55,886] [INFO] DFAST_QC completed!
[2024-01-24 14:13:55,886] [INFO] Total running time: 0h1m9s