[2024-01-24 11:43:25,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference
[2024-01-24 11:43:30,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,057] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f33e1b3-0c51-4721-8e16-21c0fd348ca5/GCF_002806945.1_ASM280694v1_genomic.fna.gz | prodigal -d GCF_002806945.1_ASM280694v1_genomic.fna/cds.fna -a GCF_002806945.1_ASM280694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:41,454] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:41,455] [INFO] Task started: HMMsearch
[2024-01-24 11:43:41,455] [INFO] Running command: hmmsearch --tblout GCF_002806945.1_ASM280694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference/reference_markers.hmm GCF_002806945.1_ASM280694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:41,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:41,737] [INFO] Found 6/6 markers.
[2024-01-24 11:43:41,771] [INFO] Query marker FASTA was written to GCF_002806945.1_ASM280694v1_genomic.fna/markers.fasta
[2024-01-24 11:43:41,771] [INFO] Task started: Blastn
[2024-01-24 11:43:41,771] [INFO] Running command: blastn -query GCF_002806945.1_ASM280694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference/reference_markers.fasta -out GCF_002806945.1_ASM280694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:42,591] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:42,594] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:42,594] [INFO] Target genome list was writen to GCF_002806945.1_ASM280694v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:42,600] [INFO] Task started: fastANI
[2024-01-24 11:43:42,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f33e1b3-0c51-4721-8e16-21c0fd348ca5/GCF_002806945.1_ASM280694v1_genomic.fna.gz --refList GCF_002806945.1_ASM280694v1_genomic.fna/target_genomes.txt --output GCF_002806945.1_ASM280694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:52,527] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:52,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:52,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:52,545] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:52,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:52,545] [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 salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	100.0	1256	1258	95	conclusive
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	81.191	817	1258	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	81.1351	806	1258	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	80.7324	758	1258	95	below_threshold
Marinobacter piscensis	strain=Abdou3	GCA_007671655.1	1562308	1562308	type	True	79.7943	567	1258	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	78.6281	359	1258	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.614	383	1258	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	78.6019	380	1258	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.5055	350	1258	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.4449	385	1258	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.4269	355	1258	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.1728	329	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:52,547] [INFO] DFAST Taxonomy check result was written to GCF_002806945.1_ASM280694v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:52,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:52,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:52,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference/checkm_data
[2024-01-24 11:43:52,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:52,589] [INFO] Task started: CheckM
[2024-01-24 11:43:52,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002806945.1_ASM280694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002806945.1_ASM280694v1_genomic.fna/checkm_input GCF_002806945.1_ASM280694v1_genomic.fna/checkm_result
[2024-01-24 11:44:29,492] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:29,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:29,515] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:29,515] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:29,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002806945.1_ASM280694v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:29,516] [INFO] Task started: Blastn
[2024-01-24 11:44:29,516] [INFO] Running command: blastn -query GCF_002806945.1_ASM280694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2be130f0-db24-45c6-826f-edc7466449cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002806945.1_ASM280694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:30,728] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:30,732] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:30,732] [INFO] Target genome list was writen to GCF_002806945.1_ASM280694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:30,741] [INFO] Task started: fastANI
[2024-01-24 11:44:30,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f33e1b3-0c51-4721-8e16-21c0fd348ca5/GCF_002806945.1_ASM280694v1_genomic.fna.gz --refList GCF_002806945.1_ASM280694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002806945.1_ASM280694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:40,831] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:40,841] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:40,842] [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_002806945.1	s__Marinobacter salexigens	100.0	1256	1258	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_016597815.1	s__Marinobacter sp016597815	84.2993	961	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.88	97.88	0.89	0.89	2	-
GCF_016597725.1	s__Marinobacter sp016597725	81.6686	814	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860765.1	s__Marinobacter salexigens_A	81.3792	761	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671675.1	s__Marinobacter maritimus	81.1767	820	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCF_001858325.1	s__Marinobacter sp001858325	81.1481	767	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.26	95.26	0.85	0.85	2	-
GCF_002806975.1	s__Marinobacter aromaticivorans	81.1269	807	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018066865.1	s__Marinobacter sp018066865	81.0887	652	1258	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	80.716	760	1258	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	80.249	760	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.10	97.17	0.88	0.86	3	-
GCF_002407605.1	s__Marinobacter sp002407605	80.0138	660	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011049865.1	s__Marinobacter antarcticus_A	79.8035	588	1258	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 11:44:40,843] [INFO] GTDB search result was written to GCF_002806945.1_ASM280694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:40,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:40,847] [INFO] DFAST_QC result json was written to GCF_002806945.1_ASM280694v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:40,847] [INFO] DFAST_QC completed!
[2024-01-24 11:44:40,847] [INFO] Total running time: 0h1m16s