[2023-06-28 02:21:56,367] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:21:56,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:21:56,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference
[2023-06-28 02:21:57,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:21:57,577] [INFO] Task started: Prodigal
[2023-06-28 02:21:57,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg53ed919c-cce2-4af6-90aa-ca4d674d3255/GCA_017391065.1_ASM1739106v1_genomic.fna.gz | prodigal -d GCA_017391065.1_ASM1739106v1_genomic.fna/cds.fna -a GCA_017391065.1_ASM1739106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:22:03,485] [INFO] Task succeeded: Prodigal
[2023-06-28 02:22:03,485] [INFO] Task started: HMMsearch
[2023-06-28 02:22:03,485] [INFO] Running command: hmmsearch --tblout GCA_017391065.1_ASM1739106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference/reference_markers.hmm GCA_017391065.1_ASM1739106v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:22:03,720] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:22:03,722] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg53ed919c-cce2-4af6-90aa-ca4d674d3255/GCA_017391065.1_ASM1739106v1_genomic.fna.gz]
[2023-06-28 02:22:03,746] [INFO] Query marker FASTA was written to GCA_017391065.1_ASM1739106v1_genomic.fna/markers.fasta
[2023-06-28 02:22:03,747] [INFO] Task started: Blastn
[2023-06-28 02:22:03,747] [INFO] Running command: blastn -query GCA_017391065.1_ASM1739106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference/reference_markers.fasta -out GCA_017391065.1_ASM1739106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:04,368] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:04,372] [INFO] Selected 26 target genomes.
[2023-06-28 02:22:04,373] [INFO] Target genome list was writen to GCA_017391065.1_ASM1739106v1_genomic.fna/target_genomes.txt
[2023-06-28 02:22:04,374] [INFO] Task started: fastANI
[2023-06-28 02:22:04,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ed919c-cce2-4af6-90aa-ca4d674d3255/GCA_017391065.1_ASM1739106v1_genomic.fna.gz --refList GCA_017391065.1_ASM1739106v1_genomic.fna/target_genomes.txt --output GCA_017391065.1_ASM1739106v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:16,656] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:16,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:16,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:16,659] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:16,659] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:22:16,660] [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
--------------------------------------------------------------------------------
[2023-06-28 02:22:16,662] [INFO] DFAST Taxonomy check result was written to GCA_017391065.1_ASM1739106v1_genomic.fna/tc_result.tsv
[2023-06-28 02:22:16,663] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:16,664] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:16,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference/checkm_data
[2023-06-28 02:22:16,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:16,697] [INFO] Task started: CheckM
[2023-06-28 02:22:16,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017391065.1_ASM1739106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017391065.1_ASM1739106v1_genomic.fna/checkm_input GCA_017391065.1_ASM1739106v1_genomic.fna/checkm_result
[2023-06-28 02:22:41,816] [INFO] Task succeeded: CheckM
[2023-06-28 02:22:41,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.27%
Contamintation: 19.57%
Strain heterogeneity: 26.92%
--------------------------------------------------------------------------------
[2023-06-28 02:22:41,843] [INFO] ===== Completeness check finished =====
[2023-06-28 02:22:41,844] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:22:41,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017391065.1_ASM1739106v1_genomic.fna/markers.fasta)
[2023-06-28 02:22:41,844] [INFO] Task started: Blastn
[2023-06-28 02:22:41,844] [INFO] Running command: blastn -query GCA_017391065.1_ASM1739106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbabe1e0e-a8bf-4800-8f76-3df1630a18d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_017391065.1_ASM1739106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:42,825] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:42,830] [INFO] Selected 29 target genomes.
[2023-06-28 02:22:42,830] [INFO] Target genome list was writen to GCA_017391065.1_ASM1739106v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:22:42,840] [INFO] Task started: fastANI
[2023-06-28 02:22:42,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ed919c-cce2-4af6-90aa-ca4d674d3255/GCA_017391065.1_ASM1739106v1_genomic.fna.gz --refList GCA_017391065.1_ASM1739106v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017391065.1_ASM1739106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:22:52,474] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:52,495] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 02:22:52,496] [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_017378975.1	s__Faecousia sp017378975	98.159	360	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017456045.1	s__Faecousia sp017456045	81.7504	237	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017457285.1	s__Faecousia sp017457285	79.6511	151	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067605.1	s__Faecousia sp015067605	79.3426	162	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.22	98.22	0.84	0.84	2	-
GCA_017456645.1	s__Faecousia sp017456645	79.2429	104	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501695.1	s__Faecousia sp017501695	79.0256	134	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465745.1	s__Faecousia sp017465745	78.8868	161	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461445.1	s__Faecousia sp017461445	78.6539	164	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562395.1	s__Faecousia sp004562395	78.6352	124	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622295.1	s__Faecousia sp017622295	78.6246	127	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067615.1	s__Faecousia sp015067615	78.584	151	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507425.1	s__Faecousia sp017507425	78.4345	140	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546075.1	s__Faecousia sp900546075	78.2523	108	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.06	96.74	0.84	0.78	6	-
GCA_000434635.1	s__Faecousia sp000434635	77.9168	113	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.30	97.16	0.81	0.81	4	-
GCA_017473455.1	s__Faecousia sp017473455	77.7881	116	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	76.7811	58	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435425.1	s__Evtepia sp017435425	76.6583	58	494	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.49	98.49	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-28 02:22:52,498] [INFO] GTDB search result was written to GCA_017391065.1_ASM1739106v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:22:52,498] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:22:52,501] [INFO] DFAST_QC result json was written to GCA_017391065.1_ASM1739106v1_genomic.fna/dqc_result.json
[2023-06-28 02:22:52,501] [INFO] DFAST_QC completed!
[2023-06-28 02:22:52,501] [INFO] Total running time: 0h0m56s