[2023-06-05 00:01:52,666] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:01:52,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:01:52,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference
[2023-06-05 00:01:53,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:01:53,973] [INFO] Task started: Prodigal
[2023-06-05 00:01:53,974] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc4affe8-9bd1-4254-a5a3-08968671b76a/GCA_004559965.1_ASM455996v1_genomic.fna.gz | prodigal -d GCA_004559965.1_ASM455996v1_genomic.fna/cds.fna -a GCA_004559965.1_ASM455996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:01:57,677] [INFO] Task succeeded: Prodigal
[2023-06-05 00:01:57,678] [INFO] Task started: HMMsearch
[2023-06-05 00:01:57,678] [INFO] Running command: hmmsearch --tblout GCA_004559965.1_ASM455996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference/reference_markers.hmm GCA_004559965.1_ASM455996v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:01:57,905] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:01:57,906] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc4affe8-9bd1-4254-a5a3-08968671b76a/GCA_004559965.1_ASM455996v1_genomic.fna.gz]
[2023-06-05 00:01:57,927] [INFO] Query marker FASTA was written to GCA_004559965.1_ASM455996v1_genomic.fna/markers.fasta
[2023-06-05 00:01:57,928] [INFO] Task started: Blastn
[2023-06-05 00:01:57,928] [INFO] Running command: blastn -query GCA_004559965.1_ASM455996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference/reference_markers.fasta -out GCA_004559965.1_ASM455996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:01:58,414] [INFO] Task succeeded: Blastn
[2023-06-05 00:01:58,418] [INFO] Selected 11 target genomes.
[2023-06-05 00:01:58,419] [INFO] Target genome list was writen to GCA_004559965.1_ASM455996v1_genomic.fna/target_genomes.txt
[2023-06-05 00:01:58,422] [INFO] Task started: fastANI
[2023-06-05 00:01:58,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc4affe8-9bd1-4254-a5a3-08968671b76a/GCA_004559965.1_ASM455996v1_genomic.fna.gz --refList GCA_004559965.1_ASM455996v1_genomic.fna/target_genomes.txt --output GCA_004559965.1_ASM455996v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:02:05,074] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:05,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:02:05,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:02:05,077] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:02:05,078] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:02:05,078] [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 00:02:05,081] [INFO] DFAST Taxonomy check result was written to GCA_004559965.1_ASM455996v1_genomic.fna/tc_result.tsv
[2023-06-05 00:02:05,082] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:02:05,082] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:02:05,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference/checkm_data
[2023-06-05 00:02:05,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:02:05,112] [INFO] Task started: CheckM
[2023-06-05 00:02:05,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004559965.1_ASM455996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004559965.1_ASM455996v1_genomic.fna/checkm_input GCA_004559965.1_ASM455996v1_genomic.fna/checkm_result
[2023-06-05 00:02:23,883] [INFO] Task succeeded: CheckM
[2023-06-05 00:02:23,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:02:23,903] [INFO] ===== Completeness check finished =====
[2023-06-05 00:02:23,903] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:02:23,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004559965.1_ASM455996v1_genomic.fna/markers.fasta)
[2023-06-05 00:02:23,904] [INFO] Task started: Blastn
[2023-06-05 00:02:23,904] [INFO] Running command: blastn -query GCA_004559965.1_ASM455996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18e62ef0-0c3d-4314-93fc-0bdd4d5cc6b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_004559965.1_ASM455996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:24,356] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:24,361] [INFO] Selected 13 target genomes.
[2023-06-05 00:02:24,362] [INFO] Target genome list was writen to GCA_004559965.1_ASM455996v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:02:24,367] [INFO] Task started: fastANI
[2023-06-05 00:02:24,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc4affe8-9bd1-4254-a5a3-08968671b76a/GCA_004559965.1_ASM455996v1_genomic.fna.gz --refList GCA_004559965.1_ASM455996v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004559965.1_ASM455996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:02:29,792] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:29,804] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:02:29,804] [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_900768995.1	s__CAG-353 sp900768995	94.9433	292	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	95.84	95.84	0.78	0.78	2	-
GCA_017829005.1	s__CAG-353 sp017829005	82.5256	260	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848125.1	s__CAG-353 sp017848125	80.4547	194	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018110855.1	s__CAG-353 sp018110855	80.4133	205	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363145.1	s__CAG-353 sp900066885	79.9675	182	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	98.51	98.32	0.91	0.87	6	-
GCA_900556055.1	s__UMGS1889 sp900556055	78.1787	62	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1889	95.0	98.05	98.05	0.88	0.88	2	-
GCA_017828975.1	s__UMGS1889 sp017828975	77.3151	79	375	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1889	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:02:29,807] [INFO] GTDB search result was written to GCA_004559965.1_ASM455996v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:02:29,807] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:02:29,810] [INFO] DFAST_QC result json was written to GCA_004559965.1_ASM455996v1_genomic.fna/dqc_result.json
[2023-06-05 00:02:29,810] [INFO] DFAST_QC completed!
[2023-06-05 00:02:29,810] [INFO] Total running time: 0h0m37s