[2023-06-29 19:13:49,703] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:49,705] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:49,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference
[2023-06-29 19:13:50,990] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:50,991] [INFO] Task started: Prodigal
[2023-06-29 19:13:50,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg904f0d33-22ac-4e4f-8cf5-e71b062eca10/GCA_023438255.1_ASM2343825v1_genomic.fna.gz | prodigal -d GCA_023438255.1_ASM2343825v1_genomic.fna/cds.fna -a GCA_023438255.1_ASM2343825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:55,467] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:55,468] [INFO] Task started: HMMsearch
[2023-06-29 19:13:55,468] [INFO] Running command: hmmsearch --tblout GCA_023438255.1_ASM2343825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference/reference_markers.hmm GCA_023438255.1_ASM2343825v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:55,709] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:55,711] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg904f0d33-22ac-4e4f-8cf5-e71b062eca10/GCA_023438255.1_ASM2343825v1_genomic.fna.gz]
[2023-06-29 19:13:55,738] [INFO] Query marker FASTA was written to GCA_023438255.1_ASM2343825v1_genomic.fna/markers.fasta
[2023-06-29 19:13:55,739] [INFO] Task started: Blastn
[2023-06-29 19:13:55,739] [INFO] Running command: blastn -query GCA_023438255.1_ASM2343825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference/reference_markers.fasta -out GCA_023438255.1_ASM2343825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:56,327] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:56,331] [INFO] Selected 12 target genomes.
[2023-06-29 19:13:56,331] [INFO] Target genome list was writen to GCA_023438255.1_ASM2343825v1_genomic.fna/target_genomes.txt
[2023-06-29 19:13:56,332] [INFO] Task started: fastANI
[2023-06-29 19:13:56,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg904f0d33-22ac-4e4f-8cf5-e71b062eca10/GCA_023438255.1_ASM2343825v1_genomic.fna.gz --refList GCA_023438255.1_ASM2343825v1_genomic.fna/target_genomes.txt --output GCA_023438255.1_ASM2343825v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:03,574] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:03,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:03,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:03,591] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 19:14:03,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:14:03,591] [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 wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	98.3299	560	610	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	98.3173	543	610	95	conclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	84.9855	419	610	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.597	223	610	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	79.4816	220	610	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	79.4178	200	610	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.1692	222	610	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.1511	163	610	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.8021	52	610	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.7017	52	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:14:03,593] [INFO] DFAST Taxonomy check result was written to GCA_023438255.1_ASM2343825v1_genomic.fna/tc_result.tsv
[2023-06-29 19:14:03,594] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:03,594] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:03,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference/checkm_data
[2023-06-29 19:14:03,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:03,625] [INFO] Task started: CheckM
[2023-06-29 19:14:03,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023438255.1_ASM2343825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023438255.1_ASM2343825v1_genomic.fna/checkm_input GCA_023438255.1_ASM2343825v1_genomic.fna/checkm_result
[2023-06-29 19:14:25,026] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:25,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.77%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:25,047] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:25,047] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:25,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023438255.1_ASM2343825v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:25,048] [INFO] Task started: Blastn
[2023-06-29 19:14:25,048] [INFO] Running command: blastn -query GCA_023438255.1_ASM2343825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e430898-bc8d-4b4d-8c9f-b497e6b12961/dqc_reference/reference_markers_gtdb.fasta -out GCA_023438255.1_ASM2343825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:25,914] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:25,919] [INFO] Selected 7 target genomes.
[2023-06-29 19:14:25,919] [INFO] Target genome list was writen to GCA_023438255.1_ASM2343825v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:25,921] [INFO] Task started: fastANI
[2023-06-29 19:14:25,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg904f0d33-22ac-4e4f-8cf5-e71b062eca10/GCA_023438255.1_ASM2343825v1_genomic.fna.gz --refList GCA_023438255.1_ASM2343825v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023438255.1_ASM2343825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:31,532] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:31,542] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:14:31,543] [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_000484655.1	s__Blautia_A wexlerae	98.3173	543	610	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	conclusive
GCF_013300825.1	s__Blautia_A wexlerae_B	93.8317	507	610	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_018919065.1	s__Blautia_A sp018919065	87.0148	408	610	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_003471165.1	s__Blautia_A sp003471165	87.0138	505	610	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCA_905209435.1	s__Blautia_A sp905209435	85.1539	394	610	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_009707925.1	s__Blautia_A luti	85.0073	418	610	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCF_003477525.1	s__Blautia_A sp003477525	84.8321	435	610	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	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:31,545] [INFO] GTDB search result was written to GCA_023438255.1_ASM2343825v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:31,545] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:31,548] [INFO] DFAST_QC result json was written to GCA_023438255.1_ASM2343825v1_genomic.fna/dqc_result.json
[2023-06-29 19:14:31,548] [INFO] DFAST_QC completed!
[2023-06-29 19:14:31,548] [INFO] Total running time: 0h0m42s