[2023-06-05 04:14:03,471] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:14:03,474] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:14:03,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference
[2023-06-05 04:14:04,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:14:04,989] [INFO] Task started: Prodigal
[2023-06-05 04:14:04,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fa789ab-4be6-4305-99de-15727e0666c8/GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna.gz | prodigal -d GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/cds.fna -a GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:14:10,077] [INFO] Task succeeded: Prodigal
[2023-06-05 04:14:10,077] [INFO] Task started: HMMsearch
[2023-06-05 04:14:10,077] [INFO] Running command: hmmsearch --tblout GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference/reference_markers.hmm GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:14:10,364] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:14:10,365] [INFO] Found 6/6 markers.
[2023-06-05 04:14:10,393] [INFO] Query marker FASTA was written to GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/markers.fasta
[2023-06-05 04:14:10,394] [INFO] Task started: Blastn
[2023-06-05 04:14:10,394] [INFO] Running command: blastn -query GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/markers.fasta -db /var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference/reference_markers.fasta -out GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:11,013] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:11,016] [INFO] Selected 31 target genomes.
[2023-06-05 04:14:11,017] [INFO] Target genome list was writen to GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/target_genomes.txt
[2023-06-05 04:14:11,019] [INFO] Task started: fastANI
[2023-06-05 04:14:11,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa789ab-4be6-4305-99de-15727e0666c8/GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna.gz --refList GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/target_genomes.txt --output GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:14:31,023] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:31,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:14:31,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:14:31,025] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:14:31,025] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:14:31,025] [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
--------------------------------------------------------------------------------
[2023-06-05 04:14:31,026] [INFO] DFAST Taxonomy check result was written to GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/tc_result.tsv
[2023-06-05 04:14:31,027] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:14:31,027] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:14:31,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference/checkm_data
[2023-06-05 04:14:31,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:14:31,058] [INFO] Task started: CheckM
[2023-06-05 04:14:31,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/checkm_input GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/checkm_result
[2023-06-05 04:14:53,071] [INFO] Task succeeded: CheckM
[2023-06-05 04:14:53,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.98%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:14:53,092] [INFO] ===== Completeness check finished =====
[2023-06-05 04:14:53,092] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:14:53,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/markers.fasta)
[2023-06-05 04:14:53,093] [INFO] Task started: Blastn
[2023-06-05 04:14:53,093] [INFO] Running command: blastn -query GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/markers.fasta -db /var/lib/cwl/stg92655f5e-c81e-4770-9fad-8c9ed6754b22/dqc_reference/reference_markers_gtdb.fasta -out GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:53,900] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:53,904] [INFO] Selected 18 target genomes.
[2023-06-05 04:14:53,905] [INFO] Target genome list was writen to GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:14:53,917] [INFO] Task started: fastANI
[2023-06-05 04:14:53,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa789ab-4be6-4305-99de-15727e0666c8/GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna.gz --refList GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/target_genomes_gtdb.txt --output GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:15:01,490] [INFO] Task succeeded: fastANI
[2023-06-05 04:15:01,501] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:15:01,502] [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_902783455.1	s__UBA3766 sp902783455	100.0	627	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902789265.1	s__UBA3766 sp902789265	80.3499	339	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	97.70	95.58	0.81	0.77	4	-
GCA_900313265.1	s__UBA3766 sp900313265	78.6177	173	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	98.28	97.21	0.86	0.74	8	-
GCA_902803015.1	s__UBA3766 sp902803015	78.563	179	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	98.47	98.47	0.83	0.83	2	-
GCA_002368665.1	s__UBA3766 sp002368665	78.1223	198	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	99.18	97.90	0.96	0.92	6	-
GCA_017518735.1	s__UBA3766 sp017518735	78.0241	222	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002494135.1	s__UBA3766 sp002494135	77.5234	193	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	98.65	98.65	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-05 04:15:01,503] [INFO] GTDB search result was written to GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/result_gtdb.tsv
[2023-06-05 04:15:01,504] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:15:01,506] [INFO] DFAST_QC result json was written to GCA_902783455.1_Rumen_uncultured_genome_RUG12880_genomic.fna/dqc_result.json
[2023-06-05 04:15:01,507] [INFO] DFAST_QC completed!
[2023-06-05 04:15:01,507] [INFO] Total running time: 0h0m58s