[2023-06-13 20:24:47,292] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:24:47,294] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:24:47,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference
[2023-06-13 20:24:48,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:24:48,470] [INFO] Task started: Prodigal
[2023-06-13 20:24:48,470] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7890431-2cd4-48ce-a51b-5b4219877b19/GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:24:53,874] [INFO] Task succeeded: Prodigal
[2023-06-13 20:24:53,875] [INFO] Task started: HMMsearch
[2023-06-13 20:24:53,875] [INFO] Running command: hmmsearch --tblout GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference/reference_markers.hmm GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:24:54,068] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:24:54,069] [INFO] Found 6/6 markers.
[2023-06-13 20:24:54,091] [INFO] Query marker FASTA was written to GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 20:24:54,091] [INFO] Task started: Blastn
[2023-06-13 20:24:54,091] [INFO] Running command: blastn -query GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference/reference_markers.fasta -out GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:54,708] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:54,712] [INFO] Selected 17 target genomes.
[2023-06-13 20:24:54,712] [INFO] Target genome list was writen to GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 20:24:54,714] [INFO] Task started: fastANI
[2023-06-13 20:24:54,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7890431-2cd4-48ce-a51b-5b4219877b19/GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:25:05,080] [INFO] Task succeeded: fastANI
[2023-06-13 20:25:05,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:25:05,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:25:05,086] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:25:05,086] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:25:05,086] [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
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	78.9897	146	778	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.5073	107	778	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.4425	99	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:25:05,088] [INFO] DFAST Taxonomy check result was written to GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 20:25:05,089] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:25:05,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:25:05,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference/checkm_data
[2023-06-13 20:25:05,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:25:05,117] [INFO] Task started: CheckM
[2023-06-13 20:25:05,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 20:25:26,477] [INFO] Task succeeded: CheckM
[2023-06-13 20:25:26,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:25:26,495] [INFO] ===== Completeness check finished =====
[2023-06-13 20:25:26,496] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:25:26,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 20:25:26,496] [INFO] Task started: Blastn
[2023-06-13 20:25:26,496] [INFO] Running command: blastn -query GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a77a1f1-db7a-46f3-9b5d-d6ee5ccaba66/dqc_reference/reference_markers_gtdb.fasta -out GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:25:27,502] [INFO] Task succeeded: Blastn
[2023-06-13 20:25:27,506] [INFO] Selected 18 target genomes.
[2023-06-13 20:25:27,506] [INFO] Target genome list was writen to GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:25:27,528] [INFO] Task started: fastANI
[2023-06-13 20:25:27,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7890431-2cd4-48ce-a51b-5b4219877b19/GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:25:35,575] [INFO] Task succeeded: fastANI
[2023-06-13 20:25:35,588] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:25:35,588] [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_000434695.1	s__Ruminococcus_D sp000434695	98.3901	656	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.00	97.86	0.87	0.86	4	conclusive
GCF_900119155.1	s__Ruminococcus_D sp900119155	78.725	218	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	99.98	99.98	0.99	0.99	2	-
GCA_902766335.1	s__Ruminococcus_D sp902766335	77.7981	191	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776945.1	s__Ruminococcus_D sp902776945	77.7878	195	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781565.1	s__Ruminococcus_D sp902781565	77.7772	185	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539095.1	s__Ruminococcus_D sp900539095	77.6569	115	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.71	97.55	0.88	0.82	3	-
GCA_017626015.1	s__Ruminococcus_D sp017626015	77.343	81	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480485.1	s__Ruminococcus_D sp017480485	77.3139	69	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112155.1	s__Ruminococcus_D albus_D	77.235	109	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797535.1	s__Ruminococcus_D sp902797535	77.1905	126	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.84	97.84	0.78	0.78	2	-
GCA_900104495.1	s__Ruminococcus_D sp900104495	77.0255	116	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752625.1	s__Ruminococcus_D sp900752625	76.9198	64	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	99.00	99.00	0.87	0.87	2	-
GCA_017478965.1	s__Ruminococcus_D sp017478965	76.9041	78	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017529875.1	s__Ruminococcus_D sp017529875	76.8954	102	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017544125.1	s__Ruminococcus_D sp017544125	76.8046	64	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786965.1	s__Ruminococcus_D sp902786965	76.6791	94	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.48	97.28	0.83	0.79	5	-
--------------------------------------------------------------------------------
[2023-06-13 20:25:35,590] [INFO] GTDB search result was written to GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 20:25:35,591] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:25:35,595] [INFO] DFAST_QC result json was written to GCA_938033145.1_ERR589843_bin.91_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 20:25:35,595] [INFO] DFAST_QC completed!
[2023-06-13 20:25:35,595] [INFO] Total running time: 0h0m48s