[2024-01-24 13:49:15,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:15,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:15,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference
[2024-01-24 13:49:17,217] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:17,218] [INFO] Task started: Prodigal
[2024-01-24 13:49:17,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg951ef73d-3389-49aa-a008-0678fb107901/GCF_002742285.1_ASM274228v1_genomic.fna.gz | prodigal -d GCF_002742285.1_ASM274228v1_genomic.fna/cds.fna -a GCF_002742285.1_ASM274228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:28,049] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:28,050] [INFO] Task started: HMMsearch
[2024-01-24 13:49:28,050] [INFO] Running command: hmmsearch --tblout GCF_002742285.1_ASM274228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference/reference_markers.hmm GCF_002742285.1_ASM274228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:28,338] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:28,339] [INFO] Found 6/6 markers.
[2024-01-24 13:49:28,372] [INFO] Query marker FASTA was written to GCF_002742285.1_ASM274228v1_genomic.fna/markers.fasta
[2024-01-24 13:49:28,372] [INFO] Task started: Blastn
[2024-01-24 13:49:28,373] [INFO] Running command: blastn -query GCF_002742285.1_ASM274228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference/reference_markers.fasta -out GCF_002742285.1_ASM274228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:29,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:29,087] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:29,088] [INFO] Target genome list was writen to GCF_002742285.1_ASM274228v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:29,107] [INFO] Task started: fastANI
[2024-01-24 13:49:29,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg951ef73d-3389-49aa-a008-0678fb107901/GCF_002742285.1_ASM274228v1_genomic.fna.gz --refList GCF_002742285.1_ASM274228v1_genomic.fna/target_genomes.txt --output GCF_002742285.1_ASM274228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:42,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:42,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:42,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:42,805] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:42,805] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:42,805] [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
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	100.0	986	987	95	conclusive
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	89.1234	856	987	95	below_threshold
Nereida ignava	strain=CECT 5292	GCA_001404155.1	282199	282199	type	True	76.9835	50	987	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	76.5701	51	987	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.3311	81	987	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.3059	55	987	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.2652	75	987	95	below_threshold
Pacificibacter marinus	strain=DSM 25228	GCA_900109555.1	658057	658057	type	True	76.2108	79	987	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	76.0478	65	987	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	75.8493	75	987	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	75.7716	53	987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:42,810] [INFO] DFAST Taxonomy check result was written to GCF_002742285.1_ASM274228v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:42,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:42,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:42,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference/checkm_data
[2024-01-24 13:49:42,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:42,846] [INFO] Task started: CheckM
[2024-01-24 13:49:42,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002742285.1_ASM274228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002742285.1_ASM274228v1_genomic.fna/checkm_input GCF_002742285.1_ASM274228v1_genomic.fna/checkm_result
[2024-01-24 13:50:20,315] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:20,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:20,333] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:20,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:20,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002742285.1_ASM274228v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:20,335] [INFO] Task started: Blastn
[2024-01-24 13:50:20,335] [INFO] Running command: blastn -query GCF_002742285.1_ASM274228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1736df2b-885d-475d-a539-ccb40c34d59d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002742285.1_ASM274228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:21,633] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:21,636] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:21,636] [INFO] Target genome list was writen to GCF_002742285.1_ASM274228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:21,651] [INFO] Task started: fastANI
[2024-01-24 13:50:21,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg951ef73d-3389-49aa-a008-0678fb107901/GCF_002742285.1_ASM274228v1_genomic.fna.gz --refList GCF_002742285.1_ASM274228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002742285.1_ASM274228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:35,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:35,096] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:35,097] [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_002742285.1	s__Amylibacter kogurei	100.0	986	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652655.1	s__Amylibacter ulvae	89.1281	855	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184395.1	s__Amylibacter sp009184395	77.7789	134	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469545.1	s__Amylibacter sp002469545	76.7621	100	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607905.1	s__Amylibacter sp002387535	76.5881	117	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.84	99.84	0.91	0.91	2	-
GCF_900107015.1	s__Litoreibacter albidus	76.5594	50	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764475.1	s__Amylibacter sp016764475	76.5047	131	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150005.2	s__Marivivens niveibacter	76.3528	80	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172335.1	s__Roseovarius albus	76.3376	54	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161835.1	s__R2A62 sp000161835	76.2872	56	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__R2A62	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744095.1	s__Shimia sp017744095	76.1274	53	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.0691	61	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852835.1	s__HIMB11 sp003486095	76.0656	60	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	98.02	97.17	0.82	0.75	18	-
GCA_013151535.1	s__UBA5972 sp013151535	76.0176	56	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900327775.1	s__Roseovarius sp900327775	75.9869	51	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706605.1	s__SAT37 sp002706605	75.8499	67	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCA_018222665.1	s__HIMB11 sp018222665	75.6804	56	987	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,098] [INFO] GTDB search result was written to GCF_002742285.1_ASM274228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:35,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:35,103] [INFO] DFAST_QC result json was written to GCF_002742285.1_ASM274228v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:35,103] [INFO] DFAST_QC completed!
[2024-01-24 13:50:35,103] [INFO] Total running time: 0h1m19s