[2024-01-24 13:55:25,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:25,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:25,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference
[2024-01-24 13:55:26,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:26,660] [INFO] Task started: Prodigal
[2024-01-24 13:55:26,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg6727f749-d94b-4b9f-a9e4-aaa129c40272/GCF_009821115.1_ASM982111v1_genomic.fna.gz | prodigal -d GCF_009821115.1_ASM982111v1_genomic.fna/cds.fna -a GCF_009821115.1_ASM982111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:37,308] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:37,308] [INFO] Task started: HMMsearch
[2024-01-24 13:55:37,308] [INFO] Running command: hmmsearch --tblout GCF_009821115.1_ASM982111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference/reference_markers.hmm GCF_009821115.1_ASM982111v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:37,616] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:37,618] [INFO] Found 6/6 markers.
[2024-01-24 13:55:37,653] [INFO] Query marker FASTA was written to GCF_009821115.1_ASM982111v1_genomic.fna/markers.fasta
[2024-01-24 13:55:37,653] [INFO] Task started: Blastn
[2024-01-24 13:55:37,653] [INFO] Running command: blastn -query GCF_009821115.1_ASM982111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference/reference_markers.fasta -out GCF_009821115.1_ASM982111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:38,337] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:38,340] [INFO] Selected 33 target genomes.
[2024-01-24 13:55:38,340] [INFO] Target genome list was writen to GCF_009821115.1_ASM982111v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:38,360] [INFO] Task started: fastANI
[2024-01-24 13:55:38,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg6727f749-d94b-4b9f-a9e4-aaa129c40272/GCF_009821115.1_ASM982111v1_genomic.fna.gz --refList GCF_009821115.1_ASM982111v1_genomic.fna/target_genomes.txt --output GCF_009821115.1_ASM982111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:58,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:58,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:58,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:58,315] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:55:58,315] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:55:58,315] [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
Nitrincola tibetensis	strain=xg18	GCA_003284585.1	2219697	2219697	type	True	88.7878	1096	1306	95	below_threshold
Nitrincola schmidtii	strain=NCAIM B.02626	GCA_008973715.1	1730894	1730894	type	True	78.3215	183	1306	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	78.3132	181	1306	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	78.197	145	1306	95	below_threshold
Nitrincola alkalilacustris	strain=NCAIM B.02612	GCA_008973755.1	1571224	1571224	type	True	77.9321	94	1306	95	below_threshold
Nitrincola tapanii	strain=MEB193	GCA_008368715.1	1708751	1708751	type	True	77.9147	140	1306	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	77.7055	58	1306	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	77.1996	70	1306	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	77.1509	70	1306	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	76.8563	60	1306	95	below_threshold
Neptunomonas antarctica	strain=DSM 22306	GCA_900156635.1	619304	619304	type	True	76.6069	59	1306	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	76.3495	56	1306	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	76.3	59	1306	95	below_threshold
Neptunomonas antarctica	strain=S3-22	GCA_001305295.1	619304	619304	type	True	76.0739	57	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:58,317] [INFO] DFAST Taxonomy check result was written to GCF_009821115.1_ASM982111v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:58,317] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:58,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:58,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference/checkm_data
[2024-01-24 13:55:58,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:58,362] [INFO] Task started: CheckM
[2024-01-24 13:55:58,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009821115.1_ASM982111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009821115.1_ASM982111v1_genomic.fna/checkm_input GCF_009821115.1_ASM982111v1_genomic.fna/checkm_result
[2024-01-24 13:56:34,035] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:34,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:34,053] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:34,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:34,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009821115.1_ASM982111v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:34,054] [INFO] Task started: Blastn
[2024-01-24 13:56:34,054] [INFO] Running command: blastn -query GCF_009821115.1_ASM982111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eb04f25-019e-483a-915f-5241d9801eb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_009821115.1_ASM982111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:34,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:34,936] [INFO] Selected 22 target genomes.
[2024-01-24 13:56:34,936] [INFO] Target genome list was writen to GCF_009821115.1_ASM982111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:34,959] [INFO] Task started: fastANI
[2024-01-24 13:56:34,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg6727f749-d94b-4b9f-a9e4-aaa129c40272/GCF_009821115.1_ASM982111v1_genomic.fna.gz --refList GCF_009821115.1_ASM982111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009821115.1_ASM982111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:48,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:48,178] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:48,178] [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_009821115.1	s__Nitrincola alkalisediminis	100.0	1305	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	99.09	99.09	0.91	0.91	2	conclusive
GCF_003284585.1	s__Nitrincola tibetensis	88.7825	1097	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973715.1	s__Nitrincola schmidtii	78.3498	184	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727795.1	s__Nitrincola sp008727795	78.3267	179	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	78.2208	144	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973755.1	s__Nitrincola alkalilacustris	77.9671	93	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008368715.1	s__Nitrincola tapanii	77.9128	140	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	77.7023	58	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCA_007693685.1	s__Nitrincola sp007693685	77.4465	134	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125745.1	s__Nitrincola sp007125745	77.2597	108	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	77.1252	52	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592555.1	s__Neptunomonas japonica_A	76.9038	58	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	76.8951	59	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305295.1	s__Neptunomonas antarctica	76.0678	57	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:48,180] [INFO] GTDB search result was written to GCF_009821115.1_ASM982111v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:48,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:48,184] [INFO] DFAST_QC result json was written to GCF_009821115.1_ASM982111v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:48,184] [INFO] DFAST_QC completed!
[2024-01-24 13:56:48,184] [INFO] Total running time: 0h1m23s