[2024-01-24 10:57:13,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference
[2024-01-24 10:57:14,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,844] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg14a5d617-ab1c-4c4c-9153-bc74728f1e5a/GCF_002806975.1_ASM280697v1_genomic.fna.gz | prodigal -d GCF_002806975.1_ASM280697v1_genomic.fna/cds.fna -a GCF_002806975.1_ASM280697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:27,646] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:27,647] [INFO] Task started: HMMsearch
[2024-01-24 10:57:27,647] [INFO] Running command: hmmsearch --tblout GCF_002806975.1_ASM280697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference/reference_markers.hmm GCF_002806975.1_ASM280697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:27,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:27,975] [INFO] Found 6/6 markers.
[2024-01-24 10:57:28,015] [INFO] Query marker FASTA was written to GCF_002806975.1_ASM280697v1_genomic.fna/markers.fasta
[2024-01-24 10:57:28,015] [INFO] Task started: Blastn
[2024-01-24 10:57:28,015] [INFO] Running command: blastn -query GCF_002806975.1_ASM280697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference/reference_markers.fasta -out GCF_002806975.1_ASM280697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:28,848] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:28,851] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:28,852] [INFO] Target genome list was writen to GCF_002806975.1_ASM280697v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:28,877] [INFO] Task started: fastANI
[2024-01-24 10:57:28,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg14a5d617-ab1c-4c4c-9153-bc74728f1e5a/GCF_002806975.1_ASM280697v1_genomic.fna.gz --refList GCF_002806975.1_ASM280697v1_genomic.fna/target_genomes.txt --output GCF_002806975.1_ASM280697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:42,250] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:42,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:42,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:42,264] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:42,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:42,265] [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 aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	100.0	1346	1349	95	conclusive
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	81.6746	857	1349	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	81.4744	807	1349	95	below_threshold
Marinobacter salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	81.2739	787	1349	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	79.4727	558	1349	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.2235	462	1349	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.9757	437	1349	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.9711	409	1349	95	below_threshold
Marinobacter salinus	strain=Hb8	GCA_001854125.1	1874317	1874317	type	True	78.9575	446	1349	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	78.934	479	1349	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.8805	468	1349	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	78.8603	394	1349	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.3612	74	1349	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	76.1671	69	1349	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.1634	68	1349	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.0776	64	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:42,268] [INFO] DFAST Taxonomy check result was written to GCF_002806975.1_ASM280697v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:42,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:42,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:42,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference/checkm_data
[2024-01-24 10:57:42,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:42,337] [INFO] Task started: CheckM
[2024-01-24 10:57:42,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002806975.1_ASM280697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002806975.1_ASM280697v1_genomic.fna/checkm_input GCF_002806975.1_ASM280697v1_genomic.fna/checkm_result
[2024-01-24 10:58:21,971] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:21,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:21,995] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:21,996] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:21,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002806975.1_ASM280697v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:21,997] [INFO] Task started: Blastn
[2024-01-24 10:58:21,997] [INFO] Running command: blastn -query GCF_002806975.1_ASM280697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f15be5f-7256-4bc5-8818-a5d824f6e9e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002806975.1_ASM280697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:23,371] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:23,375] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:23,376] [INFO] Target genome list was writen to GCF_002806975.1_ASM280697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:23,386] [INFO] Task started: fastANI
[2024-01-24 10:58:23,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg14a5d617-ab1c-4c4c-9153-bc74728f1e5a/GCF_002806975.1_ASM280697v1_genomic.fna.gz --refList GCF_002806975.1_ASM280697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002806975.1_ASM280697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:34,557] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:34,576] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:34,576] [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_002806975.1	s__Marinobacter aromaticivorans	100.0	1346	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007671675.1	s__Marinobacter maritimus	81.6746	857	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCA_018066865.1	s__Marinobacter sp018066865	81.6649	702	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.94	99.94	0.89	0.89	2	-
GCF_900142385.1	s__Marinobacter antarcticus	81.4687	808	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597815.1	s__Marinobacter sp016597815	81.2901	804	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.88	97.88	0.89	0.89	2	-
GCF_002806945.1	s__Marinobacter salexigens	81.279	786	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597725.1	s__Marinobacter sp016597725	80.9261	717	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215155.1	s__Marinobacter sp900215155	80.6738	763	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.10	97.17	0.88	0.86	3	-
GCF_018860765.1	s__Marinobacter salexigens_A	80.4477	699	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407605.1	s__Marinobacter sp002407605	80.3823	736	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318275.1	s__Marinobacter sp003318275	80.0822	589	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	79.5075	462	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	79.0338	468	1349	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 10:58:34,578] [INFO] GTDB search result was written to GCF_002806975.1_ASM280697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:34,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:34,582] [INFO] DFAST_QC result json was written to GCF_002806975.1_ASM280697v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:34,582] [INFO] DFAST_QC completed!
[2024-01-24 10:58:34,582] [INFO] Total running time: 0h1m21s