[2023-06-29 00:37:16,916] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:16,918] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:16,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference
[2023-06-29 00:37:19,513] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:19,514] [INFO] Task started: Prodigal
[2023-06-29 00:37:19,514] [INFO] Running command: gunzip -c /var/lib/cwl/stgb886a5c1-af03-4819-96d9-b83747988cae/GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:23,040] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:23,040] [INFO] Task started: HMMsearch
[2023-06-29 00:37:23,040] [INFO] Running command: hmmsearch --tblout GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference/reference_markers.hmm GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:23,333] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:23,334] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb886a5c1-af03-4819-96d9-b83747988cae/GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-29 00:37:23,377] [INFO] Query marker FASTA was written to GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-29 00:37:23,378] [INFO] Task started: Blastn
[2023-06-29 00:37:23,378] [INFO] Running command: blastn -query GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference/reference_markers.fasta -out GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:25,314] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:25,318] [INFO] Selected 12 target genomes.
[2023-06-29 00:37:25,319] [INFO] Target genome list was writen to GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 00:37:25,320] [INFO] Task started: fastANI
[2023-06-29 00:37:25,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgb886a5c1-af03-4819-96d9-b83747988cae/GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:31,851] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:31,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:31,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:31,862] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:31,862] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:37:31,863] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	80.5993	456	785	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	80.5086	465	785	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	80.1327	436	785	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.7296	385	785	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	79.6739	392	785	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	79.6227	360	785	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	79.6119	364	785	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	79.5748	356	785	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	79.4675	398	785	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	79.4119	403	785	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	78.1352	287	785	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	77.6904	222	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:37:31,865] [INFO] DFAST Taxonomy check result was written to GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 00:37:31,866] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:31,866] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:31,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference/checkm_data
[2023-06-29 00:37:31,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:31,896] [INFO] Task started: CheckM
[2023-06-29 00:37:31,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-29 00:37:54,099] [INFO] Task succeeded: CheckM
[2023-06-29 00:37:54,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:37:54,119] [INFO] ===== Completeness check finished =====
[2023-06-29 00:37:54,120] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:37:54,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 00:37:54,120] [INFO] Task started: Blastn
[2023-06-29 00:37:54,120] [INFO] Running command: blastn -query GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg790ac6e1-82e7-4bf8-8d0a-6acd659f7fd7/dqc_reference/reference_markers_gtdb.fasta -out GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:54,665] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:54,668] [INFO] Selected 8 target genomes.
[2023-06-29 00:37:54,669] [INFO] Target genome list was writen to GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:37:54,678] [INFO] Task started: fastANI
[2023-06-29 00:37:54,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgb886a5c1-af03-4819-96d9-b83747988cae/GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:00,157] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:00,177] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:00,177] [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
GCA_002685075.1	s__Poseidonibacter sp002685075	99.7435	678	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	89.1324	622	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	87.2328	578	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCA_905479135.1	s__Poseidonibacter sp905479135	84.6339	349	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	84.3683	555	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	82.9618	510	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	80.5645	459	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.5738	370	785	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:00,179] [INFO] GTDB search result was written to GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:00,180] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:00,186] [INFO] DFAST_QC result json was written to GCA_913048565.1_ERR599064_bin.82_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 00:38:00,186] [INFO] DFAST_QC completed!
[2023-06-29 00:38:00,187] [INFO] Total running time: 0h0m43s