[2023-06-08 03:31:18,265] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:31:18,268] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:31:18,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference
[2023-06-08 03:31:19,454] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:31:19,455] [INFO] Task started: Prodigal
[2023-06-08 03:31:19,455] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf09f8b3-16bf-4d18-8565-ad3a39bf5b13/GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:31:25,163] [INFO] Task succeeded: Prodigal
[2023-06-08 03:31:25,164] [INFO] Task started: HMMsearch
[2023-06-08 03:31:25,164] [INFO] Running command: hmmsearch --tblout GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference/reference_markers.hmm GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:31:25,462] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:31:25,463] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgdf09f8b3-16bf-4d18-8565-ad3a39bf5b13/GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 03:31:25,488] [INFO] Query marker FASTA was written to GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:31:25,488] [INFO] Task started: Blastn
[2023-06-08 03:31:25,488] [INFO] Running command: blastn -query GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference/reference_markers.fasta -out GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:31:25,989] [INFO] Task succeeded: Blastn
[2023-06-08 03:31:25,993] [INFO] Selected 12 target genomes.
[2023-06-08 03:31:25,993] [INFO] Target genome list was writen to GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:31:25,994] [INFO] Task started: fastANI
[2023-06-08 03:31:25,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf09f8b3-16bf-4d18-8565-ad3a39bf5b13/GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:31:32,442] [INFO] Task succeeded: fastANI
[2023-06-08 03:31:32,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:31:32,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:31:32,456] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:31:32,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:31:32,456] [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
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.5037	188	763	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.4685	194	763	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	78.3418	207	763	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	78.2574	204	763	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.2039	210	763	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	78.1385	201	763	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.8536	190	763	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.8482	212	763	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	76.6712	62	763	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	76.6427	64	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:31:32,458] [INFO] DFAST Taxonomy check result was written to GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:31:32,458] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:31:32,459] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:31:32,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference/checkm_data
[2023-06-08 03:31:32,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:31:32,487] [INFO] Task started: CheckM
[2023-06-08 03:31:32,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:31:56,594] [INFO] Task succeeded: CheckM
[2023-06-08 03:31:56,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:31:56,613] [INFO] ===== Completeness check finished =====
[2023-06-08 03:31:56,613] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:31:56,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:31:56,614] [INFO] Task started: Blastn
[2023-06-08 03:31:56,614] [INFO] Running command: blastn -query GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg570bfa14-7f8c-4572-842a-92dd4991188c/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:31:57,103] [INFO] Task succeeded: Blastn
[2023-06-08 03:31:57,108] [INFO] Selected 14 target genomes.
[2023-06-08 03:31:57,108] [INFO] Target genome list was writen to GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:31:57,114] [INFO] Task started: fastANI
[2023-06-08 03:31:57,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf09f8b3-16bf-4d18-8565-ad3a39bf5b13/GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:32:04,763] [INFO] Task succeeded: fastANI
[2023-06-08 03:32:04,778] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 03:32:04,778] [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_900541985.1	s__Blautia_A sp900541985	78.5285	193	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.92	99.92	0.93	0.93	2	-
GCF_000153905.1	s__Blautia_A obeum	78.5115	187	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	-
GCF_000484655.1	s__Blautia_A wexlerae	78.3103	200	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_009883055.1	s__Blautia_A sp900548245	78.2661	217	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.63	98.37	0.88	0.85	5	-
GCF_003477525.1	s__Blautia_A sp003477525	78.1928	186	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCA_900551715.1	s__Blautia_A sp900551715	78.1034	178	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302405.1	s__Blautia_A caecimuris	78.0478	209	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.97	96.45	0.87	0.70	11	-
GCF_016908695.1	s__Blautia_A faecis	78.0084	179	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	97.01	0.80	0.69	30	-
GCF_003461955.1	s__Blautia_A sp900066335	77.9298	203	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCA_000285855.2	s__Blautia_A sp000285855	77.8816	187	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.62	95.80	0.88	0.79	6	-
GCF_001487165.1	s__Blautia_A massiliensis	77.8536	190	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.95	95.87	0.85	0.71	55	-
GCF_013304735.1	s__Blautia_A sp900066205	77.8308	206	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCA_019116385.1	s__Blautia_A faecigallinarum	77.583	152	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120475.1	s__Blautia_A intestinipullorum	77.329	126	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.47	98.43	0.71	0.67	3	-
--------------------------------------------------------------------------------
[2023-06-08 03:32:04,780] [INFO] GTDB search result was written to GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:32:04,781] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:32:04,784] [INFO] DFAST_QC result json was written to GCA_945831385.1_SRR5240745_bin.23_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:32:04,784] [INFO] DFAST_QC completed!
[2023-06-08 03:32:04,784] [INFO] Total running time: 0h0m47s