[2023-06-04 18:46:13,089] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:46:13,094] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:46:13,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference
[2023-06-04 18:46:14,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:46:14,639] [INFO] Task started: Prodigal
[2023-06-04 18:46:14,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg023a2d39-abfa-4fed-a851-04562ae35d5a/GCA_934644945.1_ERR7747255_bin.229_genomic.fna.gz | prodigal -d GCA_934644945.1_ERR7747255_bin.229_genomic.fna/cds.fna -a GCA_934644945.1_ERR7747255_bin.229_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:46:19,807] [INFO] Task succeeded: Prodigal
[2023-06-04 18:46:19,807] [INFO] Task started: HMMsearch
[2023-06-04 18:46:19,807] [INFO] Running command: hmmsearch --tblout GCA_934644945.1_ERR7747255_bin.229_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference/reference_markers.hmm GCA_934644945.1_ERR7747255_bin.229_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:46:20,048] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:46:20,049] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg023a2d39-abfa-4fed-a851-04562ae35d5a/GCA_934644945.1_ERR7747255_bin.229_genomic.fna.gz]
[2023-06-04 18:46:20,085] [INFO] Query marker FASTA was written to GCA_934644945.1_ERR7747255_bin.229_genomic.fna/markers.fasta
[2023-06-04 18:46:20,085] [INFO] Task started: Blastn
[2023-06-04 18:46:20,086] [INFO] Running command: blastn -query GCA_934644945.1_ERR7747255_bin.229_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference/reference_markers.fasta -out GCA_934644945.1_ERR7747255_bin.229_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:46:20,855] [INFO] Task succeeded: Blastn
[2023-06-04 18:46:20,859] [INFO] Selected 28 target genomes.
[2023-06-04 18:46:20,860] [INFO] Target genome list was writen to GCA_934644945.1_ERR7747255_bin.229_genomic.fna/target_genomes.txt
[2023-06-04 18:46:20,894] [INFO] Task started: fastANI
[2023-06-04 18:46:20,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg023a2d39-abfa-4fed-a851-04562ae35d5a/GCA_934644945.1_ERR7747255_bin.229_genomic.fna.gz --refList GCA_934644945.1_ERR7747255_bin.229_genomic.fna/target_genomes.txt --output GCA_934644945.1_ERR7747255_bin.229_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:46:34,357] [INFO] Task succeeded: fastANI
[2023-06-04 18:46:34,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:46:34,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:46:34,364] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:46:34,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:46:34,364] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.1146	61	620	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.9323	55	620	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.274	61	620	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.2494	63	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:46:34,366] [INFO] DFAST Taxonomy check result was written to GCA_934644945.1_ERR7747255_bin.229_genomic.fna/tc_result.tsv
[2023-06-04 18:46:34,367] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:46:34,367] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:46:34,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference/checkm_data
[2023-06-04 18:46:34,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:46:34,395] [INFO] Task started: CheckM
[2023-06-04 18:46:34,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934644945.1_ERR7747255_bin.229_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934644945.1_ERR7747255_bin.229_genomic.fna/checkm_input GCA_934644945.1_ERR7747255_bin.229_genomic.fna/checkm_result
[2023-06-04 18:46:56,151] [INFO] Task succeeded: CheckM
[2023-06-04 18:46:56,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:46:56,173] [INFO] ===== Completeness check finished =====
[2023-06-04 18:46:56,174] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:46:56,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934644945.1_ERR7747255_bin.229_genomic.fna/markers.fasta)
[2023-06-04 18:46:56,175] [INFO] Task started: Blastn
[2023-06-04 18:46:56,175] [INFO] Running command: blastn -query GCA_934644945.1_ERR7747255_bin.229_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7a046a-de49-4948-a062-b45040f65aef/dqc_reference/reference_markers_gtdb.fasta -out GCA_934644945.1_ERR7747255_bin.229_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:46:57,398] [INFO] Task succeeded: Blastn
[2023-06-04 18:46:57,403] [INFO] Selected 13 target genomes.
[2023-06-04 18:46:57,403] [INFO] Target genome list was writen to GCA_934644945.1_ERR7747255_bin.229_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:46:57,473] [INFO] Task started: fastANI
[2023-06-04 18:46:57,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg023a2d39-abfa-4fed-a851-04562ae35d5a/GCA_934644945.1_ERR7747255_bin.229_genomic.fna.gz --refList GCA_934644945.1_ERR7747255_bin.229_genomic.fna/target_genomes_gtdb.txt --output GCA_934644945.1_ERR7747255_bin.229_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:47:03,527] [INFO] Task succeeded: fastANI
[2023-06-04 18:47:03,542] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:47:03,542] [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_900548795.1	s__Faecousia sp900548795	98.125	463	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900546415.1	s__Faecousia sp900546415	90.9112	434	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.49	97.72	0.83	0.81	4	-
GCA_905233385.1	s__Faecousia sp905233385	80.1023	235	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525905.1	s__Faecousia sp003525905	79.9538	229	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.90	97.50	0.84	0.81	6	-
GCA_017405865.1	s__Faecousia sp017405865	79.8901	218	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551495.1	s__Faecousia sp900551495	79.6869	201	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.39	98.78	0.89	0.81	3	-
GCA_900544705.1	s__Faecousia sp900544705	79.6708	239	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.60	98.49	0.88	0.86	3	-
GCA_017429835.1	s__Faecousia sp017429835	79.6606	224	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235655.1	s__Faecousia sp905235655	79.4593	195	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554705.1	s__Faecousia sp900554705	79.4549	209	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556205.1	s__Faecousia sp004556205	79.1713	176	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302005.1	s__Faecousia sp016302005	78.9078	158	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404795.1	s__CAG-170 sp002404795	78.2394	152	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	95.77	95.28	0.76	0.71	13	-
--------------------------------------------------------------------------------
[2023-06-04 18:47:03,544] [INFO] GTDB search result was written to GCA_934644945.1_ERR7747255_bin.229_genomic.fna/result_gtdb.tsv
[2023-06-04 18:47:03,545] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:47:03,548] [INFO] DFAST_QC result json was written to GCA_934644945.1_ERR7747255_bin.229_genomic.fna/dqc_result.json
[2023-06-04 18:47:03,548] [INFO] DFAST_QC completed!
[2023-06-04 18:47:03,548] [INFO] Total running time: 0h0m50s