[2024-01-24 14:30:34,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference
[2024-01-24 14:30:36,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:36,241] [INFO] Task started: Prodigal
[2024-01-24 14:30:36,241] [INFO] Running command: gunzip -c /var/lib/cwl/stga2d8f0a3-3ee6-4e0d-a47e-30e890a56969/GCF_011074795.1_ASM1107479v1_genomic.fna.gz | prodigal -d GCF_011074795.1_ASM1107479v1_genomic.fna/cds.fna -a GCF_011074795.1_ASM1107479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:49,256] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:49,257] [INFO] Task started: HMMsearch
[2024-01-24 14:30:49,257] [INFO] Running command: hmmsearch --tblout GCF_011074795.1_ASM1107479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference/reference_markers.hmm GCF_011074795.1_ASM1107479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:49,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:49,578] [INFO] Found 6/6 markers.
[2024-01-24 14:30:49,621] [INFO] Query marker FASTA was written to GCF_011074795.1_ASM1107479v1_genomic.fna/markers.fasta
[2024-01-24 14:30:49,621] [INFO] Task started: Blastn
[2024-01-24 14:30:49,622] [INFO] Running command: blastn -query GCF_011074795.1_ASM1107479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference/reference_markers.fasta -out GCF_011074795.1_ASM1107479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:50,506] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:50,509] [INFO] Selected 23 target genomes.
[2024-01-24 14:30:50,510] [INFO] Target genome list was writen to GCF_011074795.1_ASM1107479v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:50,518] [INFO] Task started: fastANI
[2024-01-24 14:30:50,518] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d8f0a3-3ee6-4e0d-a47e-30e890a56969/GCF_011074795.1_ASM1107479v1_genomic.fna.gz --refList GCF_011074795.1_ASM1107479v1_genomic.fna/target_genomes.txt --output GCF_011074795.1_ASM1107479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:07,660] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:07,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:07,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:07,677] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:07,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:07,677] [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
Marinobacter salicampi	strain=ISL-40	GCA_011074795.1	435907	435907	type	True	100.0	1429	1430	95	conclusive
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	78.7674	392	1430	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	78.6586	344	1430	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	78.647	357	1430	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.6178	359	1430	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	78.1797	318	1430	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	78.1488	339	1430	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	78.1174	304	1430	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.0673	349	1430	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	78.0558	322	1430	95	below_threshold
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	78.0555	326	1430	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	77.9876	271	1430	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	77.962	337	1430	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	77.9083	255	1430	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	77.9063	327	1430	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	77.8884	335	1430	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.8449	334	1430	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	77.8164	328	1430	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	77.8047	237	1430	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	77.7646	323	1430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:07,679] [INFO] DFAST Taxonomy check result was written to GCF_011074795.1_ASM1107479v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:07,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:07,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:07,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference/checkm_data
[2024-01-24 14:31:07,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:07,732] [INFO] Task started: CheckM
[2024-01-24 14:31:07,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011074795.1_ASM1107479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011074795.1_ASM1107479v1_genomic.fna/checkm_input GCF_011074795.1_ASM1107479v1_genomic.fna/checkm_result
[2024-01-24 14:31:49,525] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:49,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:49,548] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:49,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:49,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011074795.1_ASM1107479v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:49,549] [INFO] Task started: Blastn
[2024-01-24 14:31:49,550] [INFO] Running command: blastn -query GCF_011074795.1_ASM1107479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec18b56b-d74d-4b32-a484-cdb55cea79e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_011074795.1_ASM1107479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:50,897] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:50,901] [INFO] Selected 21 target genomes.
[2024-01-24 14:31:50,901] [INFO] Target genome list was writen to GCF_011074795.1_ASM1107479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:50,914] [INFO] Task started: fastANI
[2024-01-24 14:31:50,914] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d8f0a3-3ee6-4e0d-a47e-30e890a56969/GCF_011074795.1_ASM1107479v1_genomic.fna.gz --refList GCF_011074795.1_ASM1107479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011074795.1_ASM1107479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:07,055] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:07,078] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:07,079] [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_011074795.1	s__Marinobacter salicampi	100.0	1429	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009193265.1	s__Marinobacter changyiensis	78.7581	393	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298175.1	s__Marinobacter sp005298175	78.7123	380	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	78.6617	345	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000686085.1	s__Marinobacter sp000686085	78.4766	390	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	78.3881	363	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018334495.1	s__Marinobacter sp018334495	78.3042	299	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871205.1	s__Marinobacter alexandrii	78.1921	317	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_011074955.1	s__Marinobacter caseinilyticus	78.1493	339	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115285.1	s__Marinobacter daqiaonensis	78.1422	301	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003994855.1	s__Marinobacter sp003994855	78.1148	374	1430	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	78.0588	281	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785685.1	s__Marinobacter confluentis	78.0555	326	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002258215.1	s__Marinobacter vinifirmus	77.9725	336	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_008795985.1	s__Marinobacter halotolerans	77.9171	326	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	77.8755	337	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	77.8632	316	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCA_017643965.1	s__Marinobacter sp017643965	77.8127	277	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	77.7737	342	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_002806975.1	s__Marinobacter aromaticivorans	77.6179	252	1430	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014762755.1	s__Marinobacter sp014762755	77.4024	250	1430	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 14:32:07,081] [INFO] GTDB search result was written to GCF_011074795.1_ASM1107479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:07,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:07,086] [INFO] DFAST_QC result json was written to GCF_011074795.1_ASM1107479v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:07,086] [INFO] DFAST_QC completed!
[2024-01-24 14:32:07,086] [INFO] Total running time: 0h1m32s