[2023-06-08 01:27:38,866] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:27:38,880] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:27:38,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference
[2023-06-08 01:27:40,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:27:40,128] [INFO] Task started: Prodigal
[2023-06-08 01:27:40,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bc7775f-3e8c-4a47-8a48-b7045933e362/GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:27:45,337] [INFO] Task succeeded: Prodigal
[2023-06-08 01:27:45,337] [INFO] Task started: HMMsearch
[2023-06-08 01:27:45,337] [INFO] Running command: hmmsearch --tblout GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference/reference_markers.hmm GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:27:45,579] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:27:45,580] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9bc7775f-3e8c-4a47-8a48-b7045933e362/GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 01:27:45,612] [INFO] Query marker FASTA was written to GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 01:27:45,613] [INFO] Task started: Blastn
[2023-06-08 01:27:45,613] [INFO] Running command: blastn -query GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference/reference_markers.fasta -out GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:27:46,206] [INFO] Task succeeded: Blastn
[2023-06-08 01:27:46,209] [INFO] Selected 15 target genomes.
[2023-06-08 01:27:46,210] [INFO] Target genome list was writen to GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 01:27:46,211] [INFO] Task started: fastANI
[2023-06-08 01:27:46,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bc7775f-3e8c-4a47-8a48-b7045933e362/GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:27:54,696] [INFO] Task succeeded: fastANI
[2023-06-08 01:27:54,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:27:54,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:27:54,706] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 01:27:54,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 01:27:54,707] [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
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	97.4444	529	620	95	conclusive
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.9132	126	620	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.0286	93	620	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	76.9493	60	620	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.5861	69	620	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.1288	50	620	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.0728	53	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:27:54,723] [INFO] DFAST Taxonomy check result was written to GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 01:27:54,723] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:27:54,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:27:54,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference/checkm_data
[2023-06-08 01:27:54,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:27:54,755] [INFO] Task started: CheckM
[2023-06-08 01:27:54,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 01:28:18,387] [INFO] Task succeeded: CheckM
[2023-06-08 01:28:18,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:28:18,407] [INFO] ===== Completeness check finished =====
[2023-06-08 01:28:18,407] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:28:18,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 01:28:18,408] [INFO] Task started: Blastn
[2023-06-08 01:28:18,408] [INFO] Running command: blastn -query GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg958fd979-b379-4040-9c52-2fadfd18c6e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:28:18,868] [INFO] Task succeeded: Blastn
[2023-06-08 01:28:18,873] [INFO] Selected 10 target genomes.
[2023-06-08 01:28:18,874] [INFO] Target genome list was writen to GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:28:18,877] [INFO] Task started: fastANI
[2023-06-08 01:28:18,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bc7775f-3e8c-4a47-8a48-b7045933e362/GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:28:23,838] [INFO] Task succeeded: fastANI
[2023-06-08 01:28:23,851] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:28:23,851] [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_001406815.1	s__Agathobacter faecis	97.4444	529	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	conclusive
GCA_002474415.1	s__Agathobacter sp002474415	91.1169	400	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363675.1	s__Agathobacter sp000434275	80.4725	254	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.18	99.14	0.93	0.89	5	-
GCA_900550545.1	s__Agathobacter sp900550545	79.7928	225	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	79.4421	196	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900543445.1	s__Agathobacter sp900543445	78.3711	185	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCF_009695765.1	s__VUNI01 sp009695765	77.9132	126	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316805.1	s__Agathobacter sp900316805	77.6838	150	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.85	99.74	0.94	0.92	3	-
GCA_902363825.1	s__CAG-45 sp000438375	77.6461	90	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	-
GCA_910587655.1	s__Agathobacter sp910587655	76.8769	114	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 01:28:23,853] [INFO] GTDB search result was written to GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 01:28:23,854] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:28:23,857] [INFO] DFAST_QC result json was written to GCA_945939035.1_SRR11489785_bin.53_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 01:28:23,857] [INFO] DFAST_QC completed!
[2023-06-08 01:28:23,857] [INFO] Total running time: 0h0m45s