[2023-06-08 19:34:12,705] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:34:12,709] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:34:12,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference
[2023-06-08 19:34:13,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:34:13,943] [INFO] Task started: Prodigal
[2023-06-08 19:34:13,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a0f1e30-10e1-4a12-9692-f81f2406c7ae/GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:34:20,524] [INFO] Task succeeded: Prodigal
[2023-06-08 19:34:20,524] [INFO] Task started: HMMsearch
[2023-06-08 19:34:20,524] [INFO] Running command: hmmsearch --tblout GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference/reference_markers.hmm GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:34:20,739] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:34:20,741] [INFO] Found 6/6 markers.
[2023-06-08 19:34:20,765] [INFO] Query marker FASTA was written to GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:34:20,766] [INFO] Task started: Blastn
[2023-06-08 19:34:20,766] [INFO] Running command: blastn -query GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference/reference_markers.fasta -out GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:34:21,371] [INFO] Task succeeded: Blastn
[2023-06-08 19:34:21,375] [INFO] Selected 9 target genomes.
[2023-06-08 19:34:21,376] [INFO] Target genome list was writen to GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:34:21,377] [INFO] Task started: fastANI
[2023-06-08 19:34:21,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a0f1e30-10e1-4a12-9692-f81f2406c7ae/GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:34:25,596] [INFO] Task succeeded: fastANI
[2023-06-08 19:34:25,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:34:25,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:34:25,605] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:34:25,605] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:34:25,605] [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
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	80.0479	292	720	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	80.0102	294	720	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.0747	157	720	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.9406	167	720	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.9115	165	720	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.8653	156	720	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.4681	137	720	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.3182	116	720	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.0271	94	720	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:34:25,607] [INFO] DFAST Taxonomy check result was written to GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:34:25,608] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:34:25,608] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:34:25,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference/checkm_data
[2023-06-08 19:34:25,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:34:25,634] [INFO] Task started: CheckM
[2023-06-08 19:34:25,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:34:50,443] [INFO] Task succeeded: CheckM
[2023-06-08 19:34:50,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:34:50,465] [INFO] ===== Completeness check finished =====
[2023-06-08 19:34:50,466] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:34:50,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:34:50,466] [INFO] Task started: Blastn
[2023-06-08 19:34:50,467] [INFO] Running command: blastn -query GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d8457fe-daf6-42ed-bffe-db34fa77a4ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:34:51,409] [INFO] Task succeeded: Blastn
[2023-06-08 19:34:51,414] [INFO] Selected 12 target genomes.
[2023-06-08 19:34:51,414] [INFO] Target genome list was writen to GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:34:51,416] [INFO] Task started: fastANI
[2023-06-08 19:34:51,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a0f1e30-10e1-4a12-9692-f81f2406c7ae/GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:34:56,829] [INFO] Task succeeded: fastANI
[2023-06-08 19:34:56,844] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:34:56,844] [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_910578575.1	s__Evtepia sp910578575	99.1087	639	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910584805.1	s__Evtepia sp910584805	89.108	514	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115545.1	s__Evtepia faecavium	81.8939	317	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296565.1	s__Evtepia sp016296565	81.3742	294	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551945.1	s__Evtepia sp004551945	81.3736	352	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.68	98.58	0.91	0.88	5	-
GCA_019115225.1	s__Evtepia faecigallinarum	81.1392	341	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781745.1	s__Evtepia sp902781745	80.8629	299	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.13	97.74	0.85	0.79	11	-
GCA_900546255.1	s__Evtepia excrementipullorum	80.8457	330	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.07	97.85	0.89	0.87	5	-
GCA_004554585.1	s__Evtepia sp004554585	80.7812	356	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.56	98.47	0.94	0.93	3	-
GCA_016295225.1	s__Evtepia sp016295225	80.3106	264	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435425.1	s__Evtepia sp017435425	79.5155	300	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.49	98.49	0.92	0.92	2	-
GCA_017521345.1	s__Evtepia sp017521345	79.3365	234	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:34:56,846] [INFO] GTDB search result was written to GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:34:56,847] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:34:56,850] [INFO] DFAST_QC result json was written to GCA_947574285.1_SRR15730553_bin.43_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:34:56,850] [INFO] DFAST_QC completed!
[2023-06-08 19:34:56,850] [INFO] Total running time: 0h0m44s