[2023-06-08 19:00:58,202] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:00:58,204] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:00:58,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference
[2023-06-08 19:00:59,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:00:59,360] [INFO] Task started: Prodigal
[2023-06-08 19:00:59,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b47ffe8-9361-46f2-a5a9-b853e6936f42/GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:01:03,537] [INFO] Task succeeded: Prodigal
[2023-06-08 19:01:03,538] [INFO] Task started: HMMsearch
[2023-06-08 19:01:03,538] [INFO] Running command: hmmsearch --tblout GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference/reference_markers.hmm GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:01:03,692] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:01:03,694] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b47ffe8-9361-46f2-a5a9-b853e6936f42/GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 19:01:03,713] [INFO] Query marker FASTA was written to GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:01:03,713] [INFO] Task started: Blastn
[2023-06-08 19:01:03,713] [INFO] Running command: blastn -query GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference/reference_markers.fasta -out GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:04,261] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:04,265] [INFO] Selected 17 target genomes.
[2023-06-08 19:01:04,265] [INFO] Target genome list was writen to GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:01:04,267] [INFO] Task started: fastANI
[2023-06-08 19:01:04,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b47ffe8-9361-46f2-a5a9-b853e6936f42/GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:01:12,172] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:12,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:01:12,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:01:12,178] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:01:12,178] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:01:12,178] [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
Acutalibacter muris	strain=KB18	GCA_002201475.1	1796620	1796620	type	True	78.5829	173	427	95	below_threshold
Acutalibacter muris	strain=KB18	GCA_016697365.1	1796620	1796620	type	True	78.5387	176	427	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:01:12,180] [INFO] DFAST Taxonomy check result was written to GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:01:12,180] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:01:12,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:01:12,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference/checkm_data
[2023-06-08 19:01:12,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:01:12,202] [INFO] Task started: CheckM
[2023-06-08 19:01:12,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:01:30,538] [INFO] Task succeeded: CheckM
[2023-06-08 19:01:30,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.48%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:01:30,559] [INFO] ===== Completeness check finished =====
[2023-06-08 19:01:30,560] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:01:30,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:01:30,560] [INFO] Task started: Blastn
[2023-06-08 19:01:30,561] [INFO] Running command: blastn -query GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg662d3315-2217-4974-a7d2-3905a74111dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:31,359] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:31,363] [INFO] Selected 10 target genomes.
[2023-06-08 19:01:31,363] [INFO] Target genome list was writen to GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:01:31,364] [INFO] Task started: fastANI
[2023-06-08 19:01:31,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b47ffe8-9361-46f2-a5a9-b853e6936f42/GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:01:36,148] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:36,158] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:01:36,158] [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_910587835.1	s__Acutalibacter sp910587835	98.8334	404	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910580045.1	s__Acutalibacter sp910580045	80.977	257	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588415.1	s__Acutalibacter sp910588415	80.412	229	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587995.1	s__Acutalibacter sp910587995	80.3624	240	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612555.1	s__Acutalibacter sp003612555	79.5611	209	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201475.1	s__Acutalibacter muris	78.5829	173	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.54	97.39	0.89	0.78	6	-
GCA_900543555.1	s__Acutalibacter stercoravium	77.9394	120	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.18	97.66	0.89	0.84	11	-
GCA_019112625.1	s__Acutalibacter stercorigallinarum	77.8123	140	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	96.94	96.88	0.87	0.87	4	-
GCF_009936055.1	s__Acutalibacter sp009936055	77.6597	125	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.24	97.24	0.81	0.81	2	-
GCA_019115285.1	s__Acutalibacter pullistercoris	77.606	129	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:01:36,160] [INFO] GTDB search result was written to GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:01:36,161] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:01:36,163] [INFO] DFAST_QC result json was written to GCA_947087435.1_SRR14038233_bin.18_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:01:36,163] [INFO] DFAST_QC completed!
[2023-06-08 19:01:36,164] [INFO] Total running time: 0h0m38s