[2023-06-29 12:41:04,469] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:41:04,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:41:04,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference
[2023-06-29 12:41:05,787] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:41:05,788] [INFO] Task started: Prodigal
[2023-06-29 12:41:05,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c442f6a-e2cd-416c-8b7b-c0702daab10e/GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:41:09,897] [INFO] Task succeeded: Prodigal
[2023-06-29 12:41:09,898] [INFO] Task started: HMMsearch
[2023-06-29 12:41:09,898] [INFO] Running command: hmmsearch --tblout GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference/reference_markers.hmm GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:41:10,150] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:41:10,151] [INFO] Found 6/6 markers.
[2023-06-29 12:41:10,181] [INFO] Query marker FASTA was written to GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 12:41:10,182] [INFO] Task started: Blastn
[2023-06-29 12:41:10,182] [INFO] Running command: blastn -query GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference/reference_markers.fasta -out GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:10,790] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:10,794] [INFO] Selected 12 target genomes.
[2023-06-29 12:41:10,794] [INFO] Target genome list was writen to GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 12:41:10,796] [INFO] Task started: fastANI
[2023-06-29 12:41:10,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c442f6a-e2cd-416c-8b7b-c0702daab10e/GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:41:15,996] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:15,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:41:15,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:41:16,004] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 12:41:16,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 12:41:16,004] [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=JCM16775	GCA_007990525.1	157688	157688	type	True	95.2286	240	282	95	conclusive
Leptotrichia hofstadii	strain=DSM 21651	GCA_000428965.1	157688	157688	type	True	95.0687	245	282	95	conclusive
Leptotrichia massiliensis	strain=Marseille-P3007	GCA_900104625.1	1852388	1852388	type	True	94.4204	233	282	95	below_threshold
Leptotrichia buccalis	strain=DSM 1135	GCA_000023905.1	40542	40542	type	True	90.5248	221	282	95	below_threshold
Leptotrichia trevisanii	strain=DSM 22070	GCA_000482505.1	109328	109328	type	True	89.5157	230	282	95	below_threshold
Leptotrichia wadei	strain=DSM 19758	GCA_000373345.1	157687	157687	type	True	85.967	197	282	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:41:16,007] [INFO] DFAST Taxonomy check result was written to GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 12:41:16,007] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:41:16,007] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:41:16,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference/checkm_data
[2023-06-29 12:41:16,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:41:16,037] [INFO] Task started: CheckM
[2023-06-29 12:41:16,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 12:41:37,249] [INFO] Task succeeded: CheckM
[2023-06-29 12:41:37,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.03%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-29 12:41:37,276] [INFO] ===== Completeness check finished =====
[2023-06-29 12:41:37,277] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:41:37,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 12:41:37,278] [INFO] Task started: Blastn
[2023-06-29 12:41:37,278] [INFO] Running command: blastn -query GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a697770-11ae-4847-b89b-85c401f06b06/dqc_reference/reference_markers_gtdb.fasta -out GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:38,203] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:38,207] [INFO] Selected 11 target genomes.
[2023-06-29 12:41:38,207] [INFO] Target genome list was writen to GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:41:38,231] [INFO] Task started: fastANI
[2023-06-29 12:41:38,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c442f6a-e2cd-416c-8b7b-c0702daab10e/GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:41:42,612] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:42,631] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:41:42,632] [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_007990525.1	s__Leptotrichia hofstadii	95.1439	241	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	98.32	96.65	0.96	0.92	3	conclusive
GCF_900104625.1	s__Leptotrichia massiliensis	94.4204	233	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	96.80	96.21	0.92	0.89	3	-
GCF_000469385.1	s__Leptotrichia sp000469385	91.8546	223	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990635.1	s__Leptotrichia hongkongensis	91.4138	217	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023905.1	s__Leptotrichia buccalis	90.5779	220	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482505.1	s__Leptotrichia trevisanii	89.5157	230	282	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	89.2371	227	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274535.1	s__Leptotrichia_A sp001274535	81.6469	95	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	97.10	97.10	0.94	0.94	2	-
GCF_000469505.1	s__Leptotrichia_A sp000469505	79.8169	89	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905371725.1	s__Leptotrichia_A sp905371725	79.2416	62	282	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:41:42,634] [INFO] GTDB search result was written to GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 12:41:42,635] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:41:42,639] [INFO] DFAST_QC result json was written to GCA_937913165.1_SRR1952623_bin.28_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 12:41:42,640] [INFO] DFAST_QC completed!
[2023-06-29 12:41:42,640] [INFO] Total running time: 0h0m38s