[2023-06-29 15:33:48,899] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:33:48,902] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:33:48,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference
[2023-06-29 15:33:50,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:33:50,251] [INFO] Task started: Prodigal
[2023-06-29 15:33:50,252] [INFO] Running command: gunzip -c /var/lib/cwl/stg3aa362ad-5f97-4f2e-b0ca-a7cfd6855b48/GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:34:02,939] [INFO] Task succeeded: Prodigal
[2023-06-29 15:34:02,939] [INFO] Task started: HMMsearch
[2023-06-29 15:34:02,939] [INFO] Running command: hmmsearch --tblout GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference/reference_markers.hmm GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:34:03,206] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:34:03,207] [INFO] Found 6/6 markers.
[2023-06-29 15:34:03,242] [INFO] Query marker FASTA was written to GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 15:34:03,242] [INFO] Task started: Blastn
[2023-06-29 15:34:03,242] [INFO] Running command: blastn -query GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference/reference_markers.fasta -out GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:34:03,974] [INFO] Task succeeded: Blastn
[2023-06-29 15:34:03,978] [INFO] Selected 8 target genomes.
[2023-06-29 15:34:03,978] [INFO] Target genome list was writen to GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 15:34:03,979] [INFO] Task started: fastANI
[2023-06-29 15:34:03,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aa362ad-5f97-4f2e-b0ca-a7cfd6855b48/GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:34:12,086] [INFO] Task succeeded: fastANI
[2023-06-29 15:34:12,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:34:12,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:34:12,096] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 15:34:12,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 15:34:12,097] [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
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	98.1307	1085	1230	95	conclusive
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	97.9719	1045	1230	95	conclusive
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	87.7486	954	1230	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	87.0938	863	1230	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	86.4558	792	1230	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	86.4464	795	1230	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	86.3265	805	1230	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	83.4371	628	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:34:12,099] [INFO] DFAST Taxonomy check result was written to GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 15:34:12,100] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:34:12,100] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:34:12,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference/checkm_data
[2023-06-29 15:34:12,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:34:12,148] [INFO] Task started: CheckM
[2023-06-29 15:34:12,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 15:34:51,201] [INFO] Task succeeded: CheckM
[2023-06-29 15:34:51,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 15:34:51,225] [INFO] ===== Completeness check finished =====
[2023-06-29 15:34:51,226] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:34:51,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 15:34:51,226] [INFO] Task started: Blastn
[2023-06-29 15:34:51,226] [INFO] Running command: blastn -query GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4ecf98-8ec3-45b6-9a04-2602be28a6c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:34:52,476] [INFO] Task succeeded: Blastn
[2023-06-29 15:34:52,480] [INFO] Selected 8 target genomes.
[2023-06-29 15:34:52,481] [INFO] Target genome list was writen to GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:34:52,486] [INFO] Task started: fastANI
[2023-06-29 15:34:52,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aa362ad-5f97-4f2e-b0ca-a7cfd6855b48/GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:34:59,410] [INFO] Task succeeded: fastANI
[2023-06-29 15:34:59,417] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:34:59,418] [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_003339815.1	s__Eggerthella sinensis	98.1307	1085	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	conclusive
GCF_009834925.2	s__Eggerthella sp014287365	87.7486	954	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_900184265.1	s__Eggerthella timonensis	87.0928	864	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024265.1	s__Eggerthella lenta	86.3188	806	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_902386925.1	s__Arabia massiliensis	84.2907	672	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	83.3861	629	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCA_900170005.1	s__Gordonibacter massiliensis	83.1807	666	1230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 15:34:59,420] [INFO] GTDB search result was written to GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 15:34:59,420] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:34:59,424] [INFO] DFAST_QC result json was written to GCA_937981795.1_ERR1600608_bin.18_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 15:34:59,424] [INFO] DFAST_QC completed!
[2023-06-29 15:34:59,424] [INFO] Total running time: 0h1m11s