[2023-06-05 00:30:30,330] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:30,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:30,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference
[2023-06-05 00:30:31,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:31,628] [INFO] Task started: Prodigal
[2023-06-05 00:30:31,628] [INFO] Running command: gunzip -c /var/lib/cwl/stgffdac9c1-966f-467e-b6ab-fc33f4e67a30/GCA_001800375.1_ASM180037v1_genomic.fna.gz | prodigal -d GCA_001800375.1_ASM180037v1_genomic.fna/cds.fna -a GCA_001800375.1_ASM180037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:39,281] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:39,281] [INFO] Task started: HMMsearch
[2023-06-05 00:30:39,282] [INFO] Running command: hmmsearch --tblout GCA_001800375.1_ASM180037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference/reference_markers.hmm GCA_001800375.1_ASM180037v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:39,555] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:39,556] [INFO] Found 6/6 markers.
[2023-06-05 00:30:39,591] [INFO] Query marker FASTA was written to GCA_001800375.1_ASM180037v1_genomic.fna/markers.fasta
[2023-06-05 00:30:39,592] [INFO] Task started: Blastn
[2023-06-05 00:30:39,592] [INFO] Running command: blastn -query GCA_001800375.1_ASM180037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference/reference_markers.fasta -out GCA_001800375.1_ASM180037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:40,244] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:40,248] [INFO] Selected 15 target genomes.
[2023-06-05 00:30:40,248] [INFO] Target genome list was writen to GCA_001800375.1_ASM180037v1_genomic.fna/target_genomes.txt
[2023-06-05 00:30:40,252] [INFO] Task started: fastANI
[2023-06-05 00:30:40,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgffdac9c1-966f-467e-b6ab-fc33f4e67a30/GCA_001800375.1_ASM180037v1_genomic.fna.gz --refList GCA_001800375.1_ASM180037v1_genomic.fna/target_genomes.txt --output GCA_001800375.1_ASM180037v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:54,983] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:54,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:54,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:54,986] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:30:54,986] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:30:54,986] [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 00:30:54,988] [INFO] DFAST Taxonomy check result was written to GCA_001800375.1_ASM180037v1_genomic.fna/tc_result.tsv
[2023-06-05 00:30:54,988] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:54,988] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:54,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference/checkm_data
[2023-06-05 00:30:54,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:55,036] [INFO] Task started: CheckM
[2023-06-05 00:30:55,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001800375.1_ASM180037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001800375.1_ASM180037v1_genomic.fna/checkm_input GCA_001800375.1_ASM180037v1_genomic.fna/checkm_result
[2023-06-05 00:31:22,858] [INFO] Task succeeded: CheckM
[2023-06-05 00:31:22,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:31:22,896] [INFO] ===== Completeness check finished =====
[2023-06-05 00:31:22,896] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:31:22,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001800375.1_ASM180037v1_genomic.fna/markers.fasta)
[2023-06-05 00:31:22,897] [INFO] Task started: Blastn
[2023-06-05 00:31:22,898] [INFO] Running command: blastn -query GCA_001800375.1_ASM180037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc07eb87-46ce-41a4-bbbc-06922ff230d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_001800375.1_ASM180037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:31:23,759] [INFO] Task succeeded: Blastn
[2023-06-05 00:31:23,784] [INFO] Selected 14 target genomes.
[2023-06-05 00:31:23,785] [INFO] Target genome list was writen to GCA_001800375.1_ASM180037v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:31:23,943] [INFO] Task started: fastANI
[2023-06-05 00:31:23,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgffdac9c1-966f-467e-b6ab-fc33f4e67a30/GCA_001800375.1_ASM180037v1_genomic.fna.gz --refList GCA_001800375.1_ASM180037v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001800375.1_ASM180037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:31:31,900] [INFO] Task succeeded: fastANI
[2023-06-05 00:31:31,915] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:31:31,915] [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_001800245.1	s__YA12-FULL-51-18 sp001800245	99.902	862	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__YA12-FULL-51-18	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_001799575.1	s__YA12-FULL-51-18 sp001799575	78.2703	355	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__YA12-FULL-51-18	95.0	99.93	99.83	0.91	0.77	4	-
GCA_001799565.1	s__UBA9634 sp001799565	77.5673	138	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9634	95.0	99.92	99.83	0.96	0.96	5	-
GCA_903867985.1	s__YA12-FULL-51-18 sp903867985	77.3037	246	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__YA12-FULL-51-18	95.0	99.31	98.78	0.90	0.87	3	-
GCA_018829985.1	s__JAHJSU01 sp018829985	77.2686	198	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__JAHJSU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879915.1	s__UBA9959 sp903879915	76.8378	136	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.89	99.83	0.96	0.95	7	-
GCA_001799735.1	s__UBA9959 sp001799735	76.7946	134	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917735.1	s__UBA9959 sp903917735	76.7308	141	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208085.1	s__JAHJSU01 sp016208085	76.685	175	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__JAHJSU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482905.1	s__UBA9959 sp003482905	76.6482	139	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001871115.1	s__UBA9959 sp001871115	76.4765	99	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.77	99.67	0.95	0.95	3	-
GCA_903889965.1	s__UBA9959 sp903889965	76.2422	98	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799795.1	s__UBA9959 sp001799795	76.1207	81	1002	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:31:31,917] [INFO] GTDB search result was written to GCA_001800375.1_ASM180037v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:31:31,917] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:31:31,920] [INFO] DFAST_QC result json was written to GCA_001800375.1_ASM180037v1_genomic.fna/dqc_result.json
[2023-06-05 00:31:31,920] [INFO] DFAST_QC completed!
[2023-06-05 00:31:31,920] [INFO] Total running time: 0h1m2s