[2023-06-28 04:59:06,245] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:59:06,247] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:59:06,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference
[2023-06-28 04:59:07,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:59:07,654] [INFO] Task started: Prodigal
[2023-06-28 04:59:07,654] [INFO] Running command: gunzip -c /var/lib/cwl/stg056fe4e1-1a24-4f84-8630-db6f0be50e71/GCA_017550335.1_ASM1755033v1_genomic.fna.gz | prodigal -d GCA_017550335.1_ASM1755033v1_genomic.fna/cds.fna -a GCA_017550335.1_ASM1755033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:59:29,596] [INFO] Task succeeded: Prodigal
[2023-06-28 04:59:29,597] [INFO] Task started: HMMsearch
[2023-06-28 04:59:29,597] [INFO] Running command: hmmsearch --tblout GCA_017550335.1_ASM1755033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference/reference_markers.hmm GCA_017550335.1_ASM1755033v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:59:29,906] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:59:29,910] [INFO] Found 6/6 markers.
[2023-06-28 04:59:29,943] [INFO] Query marker FASTA was written to GCA_017550335.1_ASM1755033v1_genomic.fna/markers.fasta
[2023-06-28 04:59:29,943] [INFO] Task started: Blastn
[2023-06-28 04:59:29,943] [INFO] Running command: blastn -query GCA_017550335.1_ASM1755033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference/reference_markers.fasta -out GCA_017550335.1_ASM1755033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:30,608] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:30,613] [INFO] Selected 23 target genomes.
[2023-06-28 04:59:30,614] [INFO] Target genome list was writen to GCA_017550335.1_ASM1755033v1_genomic.fna/target_genomes.txt
[2023-06-28 04:59:30,617] [INFO] Task started: fastANI
[2023-06-28 04:59:30,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg056fe4e1-1a24-4f84-8630-db6f0be50e71/GCA_017550335.1_ASM1755033v1_genomic.fna.gz --refList GCA_017550335.1_ASM1755033v1_genomic.fna/target_genomes.txt --output GCA_017550335.1_ASM1755033v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:59:44,039] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:44,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:59:44,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:59:44,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:59:44,042] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:59:44,042] [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
--------------------------------------------------------------------------------
[2023-06-28 04:59:44,043] [INFO] DFAST Taxonomy check result was written to GCA_017550335.1_ASM1755033v1_genomic.fna/tc_result.tsv
[2023-06-28 04:59:44,044] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:59:44,044] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:59:44,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference/checkm_data
[2023-06-28 04:59:44,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:59:44,086] [INFO] Task started: CheckM
[2023-06-28 04:59:44,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017550335.1_ASM1755033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017550335.1_ASM1755033v1_genomic.fna/checkm_input GCA_017550335.1_ASM1755033v1_genomic.fna/checkm_result
[2023-06-28 05:00:46,438] [INFO] Task succeeded: CheckM
[2023-06-28 05:00:46,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:00:46,459] [INFO] ===== Completeness check finished =====
[2023-06-28 05:00:46,459] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:00:46,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017550335.1_ASM1755033v1_genomic.fna/markers.fasta)
[2023-06-28 05:00:46,460] [INFO] Task started: Blastn
[2023-06-28 05:00:46,460] [INFO] Running command: blastn -query GCA_017550335.1_ASM1755033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfab429c1-38d9-434c-a99e-174d1d2ddfb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017550335.1_ASM1755033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:00:47,298] [INFO] Task succeeded: Blastn
[2023-06-28 05:00:47,302] [INFO] Selected 6 target genomes.
[2023-06-28 05:00:47,302] [INFO] Target genome list was writen to GCA_017550335.1_ASM1755033v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:00:47,307] [INFO] Task started: fastANI
[2023-06-28 05:00:47,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg056fe4e1-1a24-4f84-8630-db6f0be50e71/GCA_017550335.1_ASM1755033v1_genomic.fna.gz --refList GCA_017550335.1_ASM1755033v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017550335.1_ASM1755033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:00:52,490] [INFO] Task succeeded: fastANI
[2023-06-28 05:00:52,499] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:00:52,500] [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_017550335.1	s__UBA1181 sp017550335	100.0	1127	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	96.84	96.79	0.92	0.92	3	conclusive
GCA_017649635.1	s__UBA1181 sp017649635	90.096	637	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962085.1	s__UBA1181 sp017962085	89.8971	863	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	98.52	98.52	0.88	0.88	2	-
GCA_017527905.1	s__UBA1181 sp017527905	89.5176	815	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310215.1	s__UBA1181 sp002310215	87.7153	784	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	98.50	97.06	0.94	0.92	3	-
GCA_016285885.1	s__UBA1181 sp016285885	87.4895	817	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:00:52,502] [INFO] GTDB search result was written to GCA_017550335.1_ASM1755033v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:00:52,503] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:00:52,505] [INFO] DFAST_QC result json was written to GCA_017550335.1_ASM1755033v1_genomic.fna/dqc_result.json
[2023-06-28 05:00:52,505] [INFO] DFAST_QC completed!
[2023-06-28 05:00:52,505] [INFO] Total running time: 0h1m46s