[2023-06-19 02:03:19,271] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:03:19,277] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:03:19,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference
[2023-06-19 02:03:20,602] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:03:20,603] [INFO] Task started: Prodigal
[2023-06-19 02:03:20,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e4041f5-db11-4adc-8ebe-0c0cf995ff14/GCA_018002475.1_ASM1800247v1_genomic.fna.gz | prodigal -d GCA_018002475.1_ASM1800247v1_genomic.fna/cds.fna -a GCA_018002475.1_ASM1800247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:03:22,793] [INFO] Task succeeded: Prodigal
[2023-06-19 02:03:22,793] [INFO] Task started: HMMsearch
[2023-06-19 02:03:22,793] [INFO] Running command: hmmsearch --tblout GCA_018002475.1_ASM1800247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference/reference_markers.hmm GCA_018002475.1_ASM1800247v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:03:23,070] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:03:23,072] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2e4041f5-db11-4adc-8ebe-0c0cf995ff14/GCA_018002475.1_ASM1800247v1_genomic.fna.gz]
[2023-06-19 02:03:23,092] [INFO] Query marker FASTA was written to GCA_018002475.1_ASM1800247v1_genomic.fna/markers.fasta
[2023-06-19 02:03:23,092] [INFO] Task started: Blastn
[2023-06-19 02:03:23,093] [INFO] Running command: blastn -query GCA_018002475.1_ASM1800247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference/reference_markers.fasta -out GCA_018002475.1_ASM1800247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:03:23,783] [INFO] Task succeeded: Blastn
[2023-06-19 02:03:23,787] [INFO] Selected 9 target genomes.
[2023-06-19 02:03:23,788] [INFO] Target genome list was writen to GCA_018002475.1_ASM1800247v1_genomic.fna/target_genomes.txt
[2023-06-19 02:03:23,789] [INFO] Task started: fastANI
[2023-06-19 02:03:23,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4041f5-db11-4adc-8ebe-0c0cf995ff14/GCA_018002475.1_ASM1800247v1_genomic.fna.gz --refList GCA_018002475.1_ASM1800247v1_genomic.fna/target_genomes.txt --output GCA_018002475.1_ASM1800247v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:03:28,754] [INFO] Task succeeded: fastANI
[2023-06-19 02:03:28,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:03:28,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:03:28,764] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2023-06-19 02:03:28,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 02:03:28,764] [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	98.778	282	295	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	98.7712	280	295	95	conclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	86.1461	219	295	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	79.6901	101	295	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.424	118	295	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.178	95	295	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.9865	50	295	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:03:28,766] [INFO] DFAST Taxonomy check result was written to GCA_018002475.1_ASM1800247v1_genomic.fna/tc_result.tsv
[2023-06-19 02:03:28,766] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:03:28,767] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:03:28,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference/checkm_data
[2023-06-19 02:03:28,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:03:28,781] [INFO] Task started: CheckM
[2023-06-19 02:03:28,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018002475.1_ASM1800247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018002475.1_ASM1800247v1_genomic.fna/checkm_input GCA_018002475.1_ASM1800247v1_genomic.fna/checkm_result
[2023-06-19 02:03:44,251] [INFO] Task succeeded: CheckM
[2023-06-19 02:03:44,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:03:44,288] [INFO] ===== Completeness check finished =====
[2023-06-19 02:03:44,288] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:03:44,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018002475.1_ASM1800247v1_genomic.fna/markers.fasta)
[2023-06-19 02:03:44,289] [INFO] Task started: Blastn
[2023-06-19 02:03:44,289] [INFO] Running command: blastn -query GCA_018002475.1_ASM1800247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg547f65aa-26f8-4b6e-bdcb-511f095b4a67/dqc_reference/reference_markers_gtdb.fasta -out GCA_018002475.1_ASM1800247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:03:44,886] [INFO] Task succeeded: Blastn
[2023-06-19 02:03:44,894] [INFO] Selected 6 target genomes.
[2023-06-19 02:03:44,894] [INFO] Target genome list was writen to GCA_018002475.1_ASM1800247v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:03:44,895] [INFO] Task started: fastANI
[2023-06-19 02:03:44,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4041f5-db11-4adc-8ebe-0c0cf995ff14/GCA_018002475.1_ASM1800247v1_genomic.fna.gz --refList GCA_018002475.1_ASM1800247v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018002475.1_ASM1800247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:03:49,017] [INFO] Task succeeded: fastANI
[2023-06-19 02:03:49,023] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-19 02:03:49,024] [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	98.7712	280	295	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	inconclusive
GCF_013300825.1	s__Blautia_A wexlerae_B	95.1155	263	295	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	inconclusive
GCF_018919065.1	s__Blautia_A sp018919065	88.3943	198	295	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_905209435.1	s__Blautia_A sp905209435	86.2338	194	295	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	86.1115	220	295	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	86.0165	234	295	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	-
--------------------------------------------------------------------------------
[2023-06-19 02:03:49,025] [INFO] GTDB search result was written to GCA_018002475.1_ASM1800247v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:03:49,026] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:03:49,029] [INFO] DFAST_QC result json was written to GCA_018002475.1_ASM1800247v1_genomic.fna/dqc_result.json
[2023-06-19 02:03:49,029] [INFO] DFAST_QC completed!
[2023-06-19 02:03:49,029] [INFO] Total running time: 0h0m30s