[2023-06-05 12:34:32,007] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:34:32,009] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:34:32,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference
[2023-06-05 12:34:33,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:34:33,106] [INFO] Task started: Prodigal
[2023-06-05 12:34:33,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg64331b00-3157-4bea-9fd4-9790614fd611/GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna.gz | prodigal -d GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/cds.fna -a GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:34:37,454] [INFO] Task succeeded: Prodigal
[2023-06-05 12:34:37,455] [INFO] Task started: HMMsearch
[2023-06-05 12:34:37,455] [INFO] Running command: hmmsearch --tblout GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference/reference_markers.hmm GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:34:37,636] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:34:37,637] [INFO] Found 6/6 markers.
[2023-06-05 12:34:37,657] [INFO] Query marker FASTA was written to GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/markers.fasta
[2023-06-05 12:34:37,657] [INFO] Task started: Blastn
[2023-06-05 12:34:37,657] [INFO] Running command: blastn -query GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference/reference_markers.fasta -out GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:34:38,187] [INFO] Task succeeded: Blastn
[2023-06-05 12:34:38,190] [INFO] Selected 25 target genomes.
[2023-06-05 12:34:38,190] [INFO] Target genome list was writen to GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/target_genomes.txt
[2023-06-05 12:34:38,231] [INFO] Task started: fastANI
[2023-06-05 12:34:38,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg64331b00-3157-4bea-9fd4-9790614fd611/GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna.gz --refList GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/target_genomes.txt --output GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:34:52,044] [INFO] Task succeeded: fastANI
[2023-06-05 12:34:52,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:34:52,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:34:52,046] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:34:52,047] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 12:34:52,047] [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 12:34:52,048] [INFO] DFAST Taxonomy check result was written to GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/tc_result.tsv
[2023-06-05 12:34:52,049] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:34:52,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:34:52,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference/checkm_data
[2023-06-05 12:34:52,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:34:52,075] [INFO] Task started: CheckM
[2023-06-05 12:34:52,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/checkm_input GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/checkm_result
[2023-06-05 12:35:11,093] [INFO] Task succeeded: CheckM
[2023-06-05 12:35:11,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 12.50%
Strain heterogeneity: 10.00%
--------------------------------------------------------------------------------
[2023-06-05 12:35:11,113] [INFO] ===== Completeness check finished =====
[2023-06-05 12:35:11,114] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:35:11,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/markers.fasta)
[2023-06-05 12:35:11,114] [INFO] Task started: Blastn
[2023-06-05 12:35:11,114] [INFO] Running command: blastn -query GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e9ca7c-333c-40dc-a2fb-eaa451bc73ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:35:11,874] [INFO] Task succeeded: Blastn
[2023-06-05 12:35:11,877] [INFO] Selected 21 target genomes.
[2023-06-05 12:35:11,878] [INFO] Target genome list was writen to GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:35:11,886] [INFO] Task started: fastANI
[2023-06-05 12:35:11,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg64331b00-3157-4bea-9fd4-9790614fd611/GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna.gz --refList GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/target_genomes_gtdb.txt --output GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:35:20,879] [INFO] Task succeeded: fastANI
[2023-06-05 12:35:20,887] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:35:20,888] [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_900319795.1	s__UBA1066 sp900319795	97.6139	501	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.52	97.64	0.89	0.84	4	conclusive
GCA_002350625.1	s__UBA1066 sp002350625	77.7576	109	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.93	99.93	0.93	0.93	2	-
GCA_902783325.1	s__UBA1066 sp902783325	77.5751	75	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430765.1	s__UBA1066 sp017430765	77.5735	63	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315305.1	s__UBA1066 sp900315305	77.537	61	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	-
GCA_902766955.1	s__UBA1066 sp902766955	77.2891	86	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.96	97.96	0.75	0.75	2	-
GCA_902776305.1	s__UBA1066 sp902776305	76.9567	60	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.81	95.96	0.86	0.75	9	-
GCA_902803505.1	s__UBA1066 sp902803505	76.88	52	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797075.1	s__UBA1066 sp902797075	76.8282	73	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773195.1	s__UBA1066 sp902773195	76.7071	66	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788035.1	s__UBA1066 sp902788035	76.6536	60	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.60	97.29	0.74	0.68	4	-
GCA_902803245.1	s__UBA1066 sp902803245	76.2655	64	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.12	98.12	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-06-05 12:35:20,889] [INFO] GTDB search result was written to GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/result_gtdb.tsv
[2023-06-05 12:35:20,890] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:35:20,893] [INFO] DFAST_QC result json was written to GCA_902781865.1_Rumen_uncultured_genome_RUG12715_genomic.fna/dqc_result.json
[2023-06-05 12:35:20,893] [INFO] DFAST_QC completed!
[2023-06-05 12:35:20,893] [INFO] Total running time: 0h0m49s