[2023-06-30 04:30:53,206] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:30:53,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:30:53,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference
[2023-06-30 04:30:54,479] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:30:54,480] [INFO] Task started: Prodigal
[2023-06-30 04:30:54,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg37d47e3f-3bcb-4b8e-b0dd-8bfbc7459e09/GCA_900758245.1_ERS608499_20_genomic.fna.gz | prodigal -d GCA_900758245.1_ERS608499_20_genomic.fna/cds.fna -a GCA_900758245.1_ERS608499_20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:30:57,612] [INFO] Task succeeded: Prodigal
[2023-06-30 04:30:57,612] [INFO] Task started: HMMsearch
[2023-06-30 04:30:57,612] [INFO] Running command: hmmsearch --tblout GCA_900758245.1_ERS608499_20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference/reference_markers.hmm GCA_900758245.1_ERS608499_20_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:30:57,820] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:30:57,822] [INFO] Found 6/6 markers.
[2023-06-30 04:30:57,845] [INFO] Query marker FASTA was written to GCA_900758245.1_ERS608499_20_genomic.fna/markers.fasta
[2023-06-30 04:30:57,845] [INFO] Task started: Blastn
[2023-06-30 04:30:57,845] [INFO] Running command: blastn -query GCA_900758245.1_ERS608499_20_genomic.fna/markers.fasta -db /var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference/reference_markers.fasta -out GCA_900758245.1_ERS608499_20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:30:58,417] [INFO] Task succeeded: Blastn
[2023-06-30 04:30:58,422] [INFO] Selected 21 target genomes.
[2023-06-30 04:30:58,423] [INFO] Target genome list was writen to GCA_900758245.1_ERS608499_20_genomic.fna/target_genomes.txt
[2023-06-30 04:30:58,427] [INFO] Task started: fastANI
[2023-06-30 04:30:58,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d47e3f-3bcb-4b8e-b0dd-8bfbc7459e09/GCA_900758245.1_ERS608499_20_genomic.fna.gz --refList GCA_900758245.1_ERS608499_20_genomic.fna/target_genomes.txt --output GCA_900758245.1_ERS608499_20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:31:09,261] [INFO] Task succeeded: fastANI
[2023-06-30 04:31:09,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:31:09,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:31:09,264] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:31:09,264] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:31:09,265] [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
--------------------------------------------------------------------------------
[2023-06-30 04:31:09,267] [INFO] DFAST Taxonomy check result was written to GCA_900758245.1_ERS608499_20_genomic.fna/tc_result.tsv
[2023-06-30 04:31:09,268] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:31:09,268] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:31:09,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference/checkm_data
[2023-06-30 04:31:09,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:31:09,294] [INFO] Task started: CheckM
[2023-06-30 04:31:09,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900758245.1_ERS608499_20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900758245.1_ERS608499_20_genomic.fna/checkm_input GCA_900758245.1_ERS608499_20_genomic.fna/checkm_result
[2023-06-30 04:31:26,508] [INFO] Task succeeded: CheckM
[2023-06-30 04:31:26,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:31:26,531] [INFO] ===== Completeness check finished =====
[2023-06-30 04:31:26,531] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:31:26,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900758245.1_ERS608499_20_genomic.fna/markers.fasta)
[2023-06-30 04:31:26,532] [INFO] Task started: Blastn
[2023-06-30 04:31:26,532] [INFO] Running command: blastn -query GCA_900758245.1_ERS608499_20_genomic.fna/markers.fasta -db /var/lib/cwl/stg3afd31d4-3605-4399-a8d1-f25159e348b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_900758245.1_ERS608499_20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:31:27,330] [INFO] Task succeeded: Blastn
[2023-06-30 04:31:27,335] [INFO] Selected 9 target genomes.
[2023-06-30 04:31:27,335] [INFO] Target genome list was writen to GCA_900758245.1_ERS608499_20_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:31:27,339] [INFO] Task started: fastANI
[2023-06-30 04:31:27,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d47e3f-3bcb-4b8e-b0dd-8bfbc7459e09/GCA_900758245.1_ERS608499_20_genomic.fna.gz --refList GCA_900758245.1_ERS608499_20_genomic.fna/target_genomes_gtdb.txt --output GCA_900758245.1_ERS608499_20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:31:30,751] [INFO] Task succeeded: fastANI
[2023-06-30 04:31:30,761] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:31:30,762] [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_900551755.1	s__Gallispira sp900551755	99.8986	453	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	99.95	99.95	0.89	0.89	2	conclusive
GCA_900543365.1	s__Gallispira sp900543365	88.9969	341	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	99.75	99.35	0.91	0.83	4	-
GCA_905201505.1	s__Gallispira sp905201505	80.1801	250	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904395805.1	s__Gallispira edinburgensis	79.6652	235	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432155.1	s__CAG-274 sp000432155	79.3877	216	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__CAG-274	95.0	98.95	98.88	0.91	0.89	4	-
GCA_900545305.1	s__CAG-274 sp900545305	78.8731	217	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__CAG-274	95.0	98.57	98.54	0.89	0.87	5	-
GCA_900760465.1	s__HGM11788 sp900760465	78.5174	151	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__HGM11788	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:31:30,764] [INFO] GTDB search result was written to GCA_900758245.1_ERS608499_20_genomic.fna/result_gtdb.tsv
[2023-06-30 04:31:30,764] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:31:30,767] [INFO] DFAST_QC result json was written to GCA_900758245.1_ERS608499_20_genomic.fna/dqc_result.json
[2023-06-30 04:31:30,767] [INFO] DFAST_QC completed!
[2023-06-30 04:31:30,767] [INFO] Total running time: 0h0m38s