[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,282] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,565] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgb03062f2-5dbd-4d87-bf3a-28e5c43e14e5/GCF_003634045.1_ASM363404v1_genomic.fna.gz | prodigal -d GCF_003634045.1_ASM363404v1_genomic.fna/cds.fna -a GCF_003634045.1_ASM363404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:35,715] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:35,716] [INFO] Task started: HMMsearch
[2024-01-24 11:48:35,716] [INFO] Running command: hmmsearch --tblout GCF_003634045.1_ASM363404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference/reference_markers.hmm GCF_003634045.1_ASM363404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:35,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:35,966] [INFO] Found 6/6 markers.
[2024-01-24 11:48:35,999] [INFO] Query marker FASTA was written to GCF_003634045.1_ASM363404v1_genomic.fna/markers.fasta
[2024-01-24 11:48:36,000] [INFO] Task started: Blastn
[2024-01-24 11:48:36,000] [INFO] Running command: blastn -query GCF_003634045.1_ASM363404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference/reference_markers.fasta -out GCF_003634045.1_ASM363404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:36,892] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:36,896] [INFO] Selected 19 target genomes.
[2024-01-24 11:48:36,897] [INFO] Target genome list was writen to GCF_003634045.1_ASM363404v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:36,906] [INFO] Task started: fastANI
[2024-01-24 11:48:36,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgb03062f2-5dbd-4d87-bf3a-28e5c43e14e5/GCF_003634045.1_ASM363404v1_genomic.fna.gz --refList GCF_003634045.1_ASM363404v1_genomic.fna/target_genomes.txt --output GCF_003634045.1_ASM363404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:49,235] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:49,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:49,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:49,251] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:48:49,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:49,251] [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
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	100.0	1180	1182	95	conclusive
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	80.6417	657	1182	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	79.3142	513	1182	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.9987	199	1182	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.8238	225	1182	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.4001	216	1182	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.3652	215	1182	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.2646	229	1182	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	77.1863	185	1182	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.9035	90	1182	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.8046	121	1182	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.7395	87	1182	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	76.6005	60	1182	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	76.4894	141	1182	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.4844	109	1182	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	76.4508	65	1182	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	75.8753	50	1182	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.8444	89	1182	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	75.8004	51	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:49,253] [INFO] DFAST Taxonomy check result was written to GCF_003634045.1_ASM363404v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:49,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:49,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:49,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference/checkm_data
[2024-01-24 11:48:49,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:49,290] [INFO] Task started: CheckM
[2024-01-24 11:48:49,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634045.1_ASM363404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634045.1_ASM363404v1_genomic.fna/checkm_input GCF_003634045.1_ASM363404v1_genomic.fna/checkm_result
[2024-01-24 11:49:42,355] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:42,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:42,371] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:42,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:42,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634045.1_ASM363404v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:42,372] [INFO] Task started: Blastn
[2024-01-24 11:49:42,372] [INFO] Running command: blastn -query GCF_003634045.1_ASM363404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbcccc8c-80f0-4317-83d1-b0ef7e8173d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634045.1_ASM363404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:44,034] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:44,038] [INFO] Selected 9 target genomes.
[2024-01-24 11:49:44,038] [INFO] Target genome list was writen to GCF_003634045.1_ASM363404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:44,047] [INFO] Task started: fastANI
[2024-01-24 11:49:44,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgb03062f2-5dbd-4d87-bf3a-28e5c43e14e5/GCF_003634045.1_ASM363404v1_genomic.fna.gz --refList GCF_003634045.1_ASM363404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634045.1_ASM363404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:51,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:51,225] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:51,227] [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_003634045.1	s__Maricaulis maris	100.0	1180	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	conclusive
GCA_015665295.1	s__Maricaulis sp015665295	85.5013	850	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	84.9629	884	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_905480005.1	s__Maricaulis sp905480005	83.3769	756	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	80.7529	660	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	80.6327	658	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	80.4342	637	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	80.4325	468	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_010975005.1	s__17J80-11 sp010975005	76.3475	137	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:51,229] [INFO] GTDB search result was written to GCF_003634045.1_ASM363404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:51,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:51,234] [INFO] DFAST_QC result json was written to GCF_003634045.1_ASM363404v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:51,234] [INFO] DFAST_QC completed!
[2024-01-24 11:49:51,234] [INFO] Total running time: 0h1m30s