[2023-06-28 01:17:56,699] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:17:56,704] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:17:56,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference
[2023-06-28 01:17:58,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:17:58,172] [INFO] Task started: Prodigal
[2023-06-28 01:17:58,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg00cdca3d-8ff3-4110-bfe0-0aacf0048c25/GCA_017627355.1_ASM1762735v1_genomic.fna.gz | prodigal -d GCA_017627355.1_ASM1762735v1_genomic.fna/cds.fna -a GCA_017627355.1_ASM1762735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:18:02,191] [INFO] Task succeeded: Prodigal
[2023-06-28 01:18:02,192] [INFO] Task started: HMMsearch
[2023-06-28 01:18:02,192] [INFO] Running command: hmmsearch --tblout GCA_017627355.1_ASM1762735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference/reference_markers.hmm GCA_017627355.1_ASM1762735v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:18:02,433] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:18:02,434] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg00cdca3d-8ff3-4110-bfe0-0aacf0048c25/GCA_017627355.1_ASM1762735v1_genomic.fna.gz]
[2023-06-28 01:18:02,453] [INFO] Query marker FASTA was written to GCA_017627355.1_ASM1762735v1_genomic.fna/markers.fasta
[2023-06-28 01:18:02,454] [INFO] Task started: Blastn
[2023-06-28 01:18:02,454] [INFO] Running command: blastn -query GCA_017627355.1_ASM1762735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference/reference_markers.fasta -out GCA_017627355.1_ASM1762735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:18:03,082] [INFO] Task succeeded: Blastn
[2023-06-28 01:18:03,085] [INFO] Selected 10 target genomes.
[2023-06-28 01:18:03,085] [INFO] Target genome list was writen to GCA_017627355.1_ASM1762735v1_genomic.fna/target_genomes.txt
[2023-06-28 01:18:03,090] [INFO] Task started: fastANI
[2023-06-28 01:18:03,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg00cdca3d-8ff3-4110-bfe0-0aacf0048c25/GCA_017627355.1_ASM1762735v1_genomic.fna.gz --refList GCA_017627355.1_ASM1762735v1_genomic.fna/target_genomes.txt --output GCA_017627355.1_ASM1762735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:18:09,834] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:09,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:18:09,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:18:09,840] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:18:09,840] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:18:09,840] [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
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	80.0705	260	561	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	78.0679	82	561	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.7779	84	561	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:18:09,842] [INFO] DFAST Taxonomy check result was written to GCA_017627355.1_ASM1762735v1_genomic.fna/tc_result.tsv
[2023-06-28 01:18:09,843] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:18:09,843] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:18:09,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference/checkm_data
[2023-06-28 01:18:09,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:18:09,870] [INFO] Task started: CheckM
[2023-06-28 01:18:09,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017627355.1_ASM1762735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017627355.1_ASM1762735v1_genomic.fna/checkm_input GCA_017627355.1_ASM1762735v1_genomic.fna/checkm_result
[2023-06-28 01:18:29,214] [INFO] Task succeeded: CheckM
[2023-06-28 01:18:29,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:18:29,239] [INFO] ===== Completeness check finished =====
[2023-06-28 01:18:29,240] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:18:29,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017627355.1_ASM1762735v1_genomic.fna/markers.fasta)
[2023-06-28 01:18:29,241] [INFO] Task started: Blastn
[2023-06-28 01:18:29,241] [INFO] Running command: blastn -query GCA_017627355.1_ASM1762735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a1a7e01-d195-4973-8933-284945b35107/dqc_reference/reference_markers_gtdb.fasta -out GCA_017627355.1_ASM1762735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:18:29,999] [INFO] Task succeeded: Blastn
[2023-06-28 01:18:30,003] [INFO] Selected 9 target genomes.
[2023-06-28 01:18:30,003] [INFO] Target genome list was writen to GCA_017627355.1_ASM1762735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:18:30,006] [INFO] Task started: fastANI
[2023-06-28 01:18:30,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg00cdca3d-8ff3-4110-bfe0-0aacf0048c25/GCA_017627355.1_ASM1762735v1_genomic.fna.gz --refList GCA_017627355.1_ASM1762735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017627355.1_ASM1762735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:18:36,104] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:36,116] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:18:36,116] [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_902792495.1	s__Ruminococcus flavefaciens_Z	96.8065	307	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.07	96.74	0.72	0.58	3	conclusive
GCF_000174895.1	s__Ruminococcus flavefaciens_A	92.3704	495	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	96.87	96.87	0.86	0.86	2	-
GCA_017418765.1	s__Ruminococcus sp017418765	86.391	212	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303195.1	s__Ruminococcus sp016303195	83.3914	256	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017479805.1	s__Ruminococcus sp017479805	82.193	315	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119075.1	s__Ruminococcus flavefaciens_Q	80.5102	257	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.02	98.02	0.91	0.91	2	-
GCA_902780115.1	s__Ruminococcus flavefaciens_Y	80.1393	183	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116855.1	s__Ruminococcus flavefaciens_R	80.0802	280	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.90	97.16	0.91	0.76	13	-
GCA_016283395.1	s__Ruminococcus sp016283395	79.941	251	561	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:18:36,118] [INFO] GTDB search result was written to GCA_017627355.1_ASM1762735v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:18:36,119] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:18:36,122] [INFO] DFAST_QC result json was written to GCA_017627355.1_ASM1762735v1_genomic.fna/dqc_result.json
[2023-06-28 01:18:36,122] [INFO] DFAST_QC completed!
[2023-06-28 01:18:36,122] [INFO] Total running time: 0h0m39s