[2023-06-08 19:01:01,010] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:01:01,012] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:01:01,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference
[2023-06-08 19:01:02,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:01:02,255] [INFO] Task started: Prodigal
[2023-06-08 19:01:02,255] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2dac7bf-40f7-4257-8456-4b5e3c171034/GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:01:05,104] [INFO] Task succeeded: Prodigal
[2023-06-08 19:01:05,105] [INFO] Task started: HMMsearch
[2023-06-08 19:01:05,105] [INFO] Running command: hmmsearch --tblout GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference/reference_markers.hmm GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:01:05,369] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:01:05,370] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc2dac7bf-40f7-4257-8456-4b5e3c171034/GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 19:01:05,396] [INFO] Query marker FASTA was written to GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:01:05,397] [INFO] Task started: Blastn
[2023-06-08 19:01:05,397] [INFO] Running command: blastn -query GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference/reference_markers.fasta -out GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:06,045] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:06,049] [INFO] Selected 14 target genomes.
[2023-06-08 19:01:06,050] [INFO] Target genome list was writen to GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:01:06,056] [INFO] Task started: fastANI
[2023-06-08 19:01:06,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2dac7bf-40f7-4257-8456-4b5e3c171034/GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:01:12,930] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:12,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:01:12,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:01:12,940] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:01:12,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:01:12,941] [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
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	82.5918	310	408	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	82.5918	310	408	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	77.1473	140	408	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	76.9295	108	408	95	below_threshold
Lonepinella koalarum	strain=DSM 10053	GCA_004339625.1	53417	53417	type	True	76.9009	129	408	95	below_threshold
Lonepinella koalarum	strain=ATCC 700131	GCA_004565475.1	53417	53417	type	True	76.898	129	408	95	below_threshold
Pasteurella dagmatis	strain=ATCC 43325	GCA_000163475.1	754	754	type	True	76.8859	110	408	95	below_threshold
Basfia succiniciproducens	strain=JF4016	GCA_011455875.1	653940	653940	suspected-type	True	76.5458	101	408	95	below_threshold
Volucribacter psittacicida	strain=DSM 15534	GCA_004339025.1	203482	203482	type	True	76.1923	82	408	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:01:12,963] [INFO] DFAST Taxonomy check result was written to GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:01:12,963] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:01:12,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:01:12,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference/checkm_data
[2023-06-08 19:01:12,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:01:12,984] [INFO] Task started: CheckM
[2023-06-08 19:01:12,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:01:29,584] [INFO] Task succeeded: CheckM
[2023-06-08 19:01:29,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:01:29,605] [INFO] ===== Completeness check finished =====
[2023-06-08 19:01:29,605] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:01:29,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:01:29,606] [INFO] Task started: Blastn
[2023-06-08 19:01:29,606] [INFO] Running command: blastn -query GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg433b04db-63f8-40ac-b6bb-338b86f4eec4/dqc_reference/reference_markers_gtdb.fasta -out GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:30,370] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:30,374] [INFO] Selected 18 target genomes.
[2023-06-08 19:01:30,374] [INFO] Target genome list was writen to GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:01:30,488] [INFO] Task started: fastANI
[2023-06-08 19:01:30,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2dac7bf-40f7-4257-8456-4b5e3c171034/GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:01:39,095] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:39,115] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:01:39,116] [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_900444965.1	s__Basfia_A rossii	95.7111	376	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_901764995.1	s__Basfia_A porcinus	82.5918	310	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003096995.1	s__Basfia_A langaaensis	79.1267	238	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262245.1	s__Basfia bettyae	77.1473	140	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
GCF_014843355.1	s__Basfia_A sp014843355	76.9643	104	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186835.1	s__Pasteurella dagmatis	76.9538	107	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_003352385.1	s__Haemophilus haemolyticus_I	76.9058	108	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.71	95.22	0.89	0.82	17	-
GCF_004565475.1	s__Lonepinella koalarum	76.898	129	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	-
GCA_001752465.1	s__Haemophilus quentini	76.8851	113	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	99.94	99.85	0.97	0.94	5	-
GCA_900454475.1	s__Actinobacillus_B mairii	76.8141	95	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340985.1	s__Cricetibacter osteomyelitidis	76.4361	83	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Cricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:01:39,119] [INFO] GTDB search result was written to GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:01:39,120] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:01:39,123] [INFO] DFAST_QC result json was written to GCA_945788085.1_SRR3173844_bin.5_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:01:39,123] [INFO] DFAST_QC completed!
[2023-06-08 19:01:39,123] [INFO] Total running time: 0h0m38s