[2024-01-25 19:45:50,522] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference
[2024-01-25 19:45:51,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,669] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,669] [INFO] Running command: gunzip -c /var/lib/cwl/stgd91a4915-4ac6-46d6-bd3c-2760c24311f7/GCF_026191375.1_ASM2619137v1_genomic.fna.gz | prodigal -d GCF_026191375.1_ASM2619137v1_genomic.fna/cds.fna -a GCF_026191375.1_ASM2619137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:59,765] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:59,765] [INFO] Task started: HMMsearch
[2024-01-25 19:45:59,765] [INFO] Running command: hmmsearch --tblout GCF_026191375.1_ASM2619137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference/reference_markers.hmm GCF_026191375.1_ASM2619137v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:00,019] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:00,020] [INFO] Found 6/6 markers.
[2024-01-25 19:46:00,054] [INFO] Query marker FASTA was written to GCF_026191375.1_ASM2619137v1_genomic.fna/markers.fasta
[2024-01-25 19:46:00,055] [INFO] Task started: Blastn
[2024-01-25 19:46:00,055] [INFO] Running command: blastn -query GCF_026191375.1_ASM2619137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference/reference_markers.fasta -out GCF_026191375.1_ASM2619137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:00,670] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:00,673] [INFO] Selected 14 target genomes.
[2024-01-25 19:46:00,673] [INFO] Target genome list was writen to GCF_026191375.1_ASM2619137v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:00,686] [INFO] Task started: fastANI
[2024-01-25 19:46:00,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgd91a4915-4ac6-46d6-bd3c-2760c24311f7/GCF_026191375.1_ASM2619137v1_genomic.fna.gz --refList GCF_026191375.1_ASM2619137v1_genomic.fna/target_genomes.txt --output GCF_026191375.1_ASM2619137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:11,930] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:11,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:11,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:11,939] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:11,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:11,939] [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
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	82.6337	757	1161	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	82.6281	771	1161	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	82.2928	772	1161	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	82.1426	719	1161	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	81.7024	725	1161	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	81.6298	721	1161	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	81.1694	708	1161	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_020694005.1	2726122	2726122	type	True	81.1078	668	1161	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	81.0995	657	1161	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	80.9935	673	1161	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	80.3744	642	1161	95	below_threshold
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	78.9945	318	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:11,940] [INFO] DFAST Taxonomy check result was written to GCF_026191375.1_ASM2619137v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:11,941] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:11,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:11,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference/checkm_data
[2024-01-25 19:46:11,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:11,978] [INFO] Task started: CheckM
[2024-01-25 19:46:11,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026191375.1_ASM2619137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026191375.1_ASM2619137v1_genomic.fna/checkm_input GCF_026191375.1_ASM2619137v1_genomic.fna/checkm_result
[2024-01-25 19:46:40,108] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:40,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:40,181] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:40,181] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:40,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026191375.1_ASM2619137v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:40,182] [INFO] Task started: Blastn
[2024-01-25 19:46:40,182] [INFO] Running command: blastn -query GCF_026191375.1_ASM2619137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e482e14-dd6a-42fb-a15a-59a4b5581591/dqc_reference/reference_markers_gtdb.fasta -out GCF_026191375.1_ASM2619137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:41,030] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:41,032] [INFO] Selected 11 target genomes.
[2024-01-25 19:46:41,033] [INFO] Target genome list was writen to GCF_026191375.1_ASM2619137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:41,058] [INFO] Task started: fastANI
[2024-01-25 19:46:41,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgd91a4915-4ac6-46d6-bd3c-2760c24311f7/GCF_026191375.1_ASM2619137v1_genomic.fna.gz --refList GCF_026191375.1_ASM2619137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026191375.1_ASM2619137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:50,684] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:50,691] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:46:50,692] [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_003337275.1	s__Marinomonas foliarum	82.634	757	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_018336955.1	s__Marinomonas sp018336955	82.5337	785	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129155.1	s__Marinomonas polaris	82.2859	773	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_003208215.1	s__Marinomonas alcarazii	82.1299	720	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_000017285.1	s__Marinomonas sp000017285	81.8161	757	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_003315485.1	s__Marinomonas rhizomae	81.7116	723	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259175.1	s__Marinomonas shanghaiensis	81.1781	707	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012584435.1	s__Marinomonas sp012584435	81.1184	655	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018336975.1	s__Marinomonas sp013373235	81.0688	662	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_000508165.1	s__Marinomonas profundimaris	80.9999	672	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372285.1	s__Marinomonas primoryensis	80.3838	641	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:50,693] [INFO] GTDB search result was written to GCF_026191375.1_ASM2619137v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:50,693] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:50,696] [INFO] DFAST_QC result json was written to GCF_026191375.1_ASM2619137v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:50,696] [INFO] DFAST_QC completed!
[2024-01-25 19:46:50,696] [INFO] Total running time: 0h1m0s