[2023-06-13 18:55:32,317] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:55:32,319] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:55:32,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference
[2023-06-13 18:55:33,515] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:55:33,516] [INFO] Task started: Prodigal
[2023-06-13 18:55:33,516] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9ded1b1-bb59-45dc-aac9-a635dc8f4a86/GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:55:37,109] [INFO] Task succeeded: Prodigal
[2023-06-13 18:55:37,109] [INFO] Task started: HMMsearch
[2023-06-13 18:55:37,109] [INFO] Running command: hmmsearch --tblout GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference/reference_markers.hmm GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:55:37,314] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:55:37,315] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9ded1b1-bb59-45dc-aac9-a635dc8f4a86/GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 18:55:37,340] [INFO] Query marker FASTA was written to GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 18:55:37,340] [INFO] Task started: Blastn
[2023-06-13 18:55:37,340] [INFO] Running command: blastn -query GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference/reference_markers.fasta -out GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:55:37,923] [INFO] Task succeeded: Blastn
[2023-06-13 18:55:37,927] [INFO] Selected 19 target genomes.
[2023-06-13 18:55:37,927] [INFO] Target genome list was writen to GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 18:55:37,930] [INFO] Task started: fastANI
[2023-06-13 18:55:37,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9ded1b1-bb59-45dc-aac9-a635dc8f4a86/GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:55:47,405] [INFO] Task succeeded: fastANI
[2023-06-13 18:55:47,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:55:47,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:55:47,414] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:55:47,414] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:55:47,414] [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
Leptotrichia hofstadii	strain=DSM 21651	GCA_000428965.1	157688	157688	type	True	91.4771	385	449	95	below_threshold
Leptotrichia hofstadii	strain=JCM16775	GCA_007990525.1	157688	157688	type	True	91.4011	392	449	95	below_threshold
Leptotrichia massiliensis	strain=Marseille-P3007	GCA_900104625.1	1852388	1852388	type	True	90.4387	386	449	95	below_threshold
Leptotrichia trevisanii	strain=DSM 22070	GCA_000482505.1	109328	109328	type	True	88.8032	393	449	95	below_threshold
Leptotrichia buccalis	strain=DSM 1135	GCA_000023905.1	40542	40542	type	True	87.5203	355	449	95	below_threshold
Leptotrichia wadei	strain=DSM 19758	GCA_000373345.1	157687	157687	type	True	85.8905	339	449	95	below_threshold
Leptotrichia wadei	strain=JCM16777	GCA_007990545.2	157687	157687	type	True	85.8709	346	449	95	below_threshold
Leptotrichia shahii	strain=DSM 19757	GCA_000373045.1	157691	157691	type	True	85.8301	335	449	95	below_threshold
Leptotrichia shahii	strain=JCM16776	GCA_008327825.1	157691	157691	type	True	85.7162	345	449	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:55:47,416] [INFO] DFAST Taxonomy check result was written to GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 18:55:47,417] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:55:47,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:55:47,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference/checkm_data
[2023-06-13 18:55:47,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:55:47,444] [INFO] Task started: CheckM
[2023-06-13 18:55:47,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 18:56:05,952] [INFO] Task succeeded: CheckM
[2023-06-13 18:56:05,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:56:05,976] [INFO] ===== Completeness check finished =====
[2023-06-13 18:56:05,976] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:56:05,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 18:56:05,977] [INFO] Task started: Blastn
[2023-06-13 18:56:05,977] [INFO] Running command: blastn -query GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd58d3d-0336-4fcd-9284-7eb6767ca3b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:56:06,755] [INFO] Task succeeded: Blastn
[2023-06-13 18:56:06,759] [INFO] Selected 19 target genomes.
[2023-06-13 18:56:06,759] [INFO] Target genome list was writen to GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:56:06,764] [INFO] Task started: fastANI
[2023-06-13 18:56:06,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9ded1b1-bb59-45dc-aac9-a635dc8f4a86/GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:56:15,853] [INFO] Task succeeded: fastANI
[2023-06-13 18:56:15,862] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:56:15,862] [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_007990635.1	s__Leptotrichia hongkongensis	95.4341	401	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000469385.1	s__Leptotrichia sp000469385	93.8021	370	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990525.1	s__Leptotrichia hofstadii	91.3748	393	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	98.32	96.65	0.96	0.92	3	-
GCF_900104625.1	s__Leptotrichia massiliensis	90.4607	387	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	96.80	96.21	0.92	0.89	3	-
GCF_000482505.1	s__Leptotrichia trevisanii	88.8338	392	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.98	97.58	0.90	0.88	4	-
GCF_013394795.1	s__Leptotrichia sp013394795	87.8354	391	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990545.2	s__Leptotrichia wadei	85.8709	346	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.52	96.88	0.90	0.86	7	-
GCF_008327825.1	s__Leptotrichia shahii	85.7466	346	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	99.96	99.96	1.00	1.00	2	-
GCF_007990445.1	s__Leptotrichia wadei_A	84.5504	347	449	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.03	96.85	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-13 18:56:15,864] [INFO] GTDB search result was written to GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 18:56:15,865] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:56:15,869] [INFO] DFAST_QC result json was written to GCA_938036635.1_ERR589621_bin.71_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 18:56:15,869] [INFO] DFAST_QC completed!
[2023-06-13 18:56:15,869] [INFO] Total running time: 0h0m44s