[2023-06-19 03:26:20,703] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:26:20,705] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:26:20,705] [INFO] DQC Reference Directory: /var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference
[2023-06-19 03:26:22,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:26:22,091] [INFO] Task started: Prodigal
[2023-06-19 03:26:22,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb92072d-0c45-43ce-89cc-07df5f1dfc1b/GCA_018385095.1_ASM1838509v1_genomic.fna.gz | prodigal -d GCA_018385095.1_ASM1838509v1_genomic.fna/cds.fna -a GCA_018385095.1_ASM1838509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:26:34,408] [INFO] Task succeeded: Prodigal
[2023-06-19 03:26:34,409] [INFO] Task started: HMMsearch
[2023-06-19 03:26:34,409] [INFO] Running command: hmmsearch --tblout GCA_018385095.1_ASM1838509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference/reference_markers.hmm GCA_018385095.1_ASM1838509v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:26:34,636] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:26:34,638] [INFO] Found 6/6 markers.
[2023-06-19 03:26:34,676] [INFO] Query marker FASTA was written to GCA_018385095.1_ASM1838509v1_genomic.fna/markers.fasta
[2023-06-19 03:26:34,676] [INFO] Task started: Blastn
[2023-06-19 03:26:34,677] [INFO] Running command: blastn -query GCA_018385095.1_ASM1838509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference/reference_markers.fasta -out GCA_018385095.1_ASM1838509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:26:35,334] [INFO] Task succeeded: Blastn
[2023-06-19 03:26:35,338] [INFO] Selected 30 target genomes.
[2023-06-19 03:26:35,338] [INFO] Target genome list was writen to GCA_018385095.1_ASM1838509v1_genomic.fna/target_genomes.txt
[2023-06-19 03:26:35,345] [INFO] Task started: fastANI
[2023-06-19 03:26:35,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb92072d-0c45-43ce-89cc-07df5f1dfc1b/GCA_018385095.1_ASM1838509v1_genomic.fna.gz --refList GCA_018385095.1_ASM1838509v1_genomic.fna/target_genomes.txt --output GCA_018385095.1_ASM1838509v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:26:51,693] [INFO] Task succeeded: fastANI
[2023-06-19 03:26:51,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:26:51,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:26:51,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:26:51,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 03:26:51,697] [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
--------------------------------------------------------------------------------
[2023-06-19 03:26:51,702] [INFO] DFAST Taxonomy check result was written to GCA_018385095.1_ASM1838509v1_genomic.fna/tc_result.tsv
[2023-06-19 03:26:51,703] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:26:51,703] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:26:51,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference/checkm_data
[2023-06-19 03:26:51,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:26:51,734] [INFO] Task started: CheckM
[2023-06-19 03:26:51,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018385095.1_ASM1838509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018385095.1_ASM1838509v1_genomic.fna/checkm_input GCA_018385095.1_ASM1838509v1_genomic.fna/checkm_result
[2023-06-19 03:27:31,451] [INFO] Task succeeded: CheckM
[2023-06-19 03:27:31,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:27:31,472] [INFO] ===== Completeness check finished =====
[2023-06-19 03:27:31,472] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:27:31,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018385095.1_ASM1838509v1_genomic.fna/markers.fasta)
[2023-06-19 03:27:31,473] [INFO] Task started: Blastn
[2023-06-19 03:27:31,473] [INFO] Running command: blastn -query GCA_018385095.1_ASM1838509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc851b734-2bc1-4a86-b5a5-2be580fe0b0a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018385095.1_ASM1838509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:27:32,442] [INFO] Task succeeded: Blastn
[2023-06-19 03:27:32,447] [INFO] Selected 21 target genomes.
[2023-06-19 03:27:32,447] [INFO] Target genome list was writen to GCA_018385095.1_ASM1838509v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:27:32,461] [INFO] Task started: fastANI
[2023-06-19 03:27:32,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb92072d-0c45-43ce-89cc-07df5f1dfc1b/GCA_018385095.1_ASM1838509v1_genomic.fna.gz --refList GCA_018385095.1_ASM1838509v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018385095.1_ASM1838509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:27:41,155] [INFO] Task succeeded: fastANI
[2023-06-19 03:27:41,170] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:27:41,170] [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_900766785.1	s__UBA4372 sp900766785	97.5764	375	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.88	97.64	0.81	0.78	8	conclusive
GCA_900543815.1	s__UBA4372 sp900543815	79.7117	281	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.82	97.58	0.92	0.88	4	-
GCA_002316015.1	s__UBA4372 sp002316015	78.3649	218	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	99.56	99.28	0.95	0.93	7	-
GCA_902775385.1	s__UBA4372 sp902775385	77.2087	71	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.32	98.32	0.92	0.92	2	-
GCA_902799985.1	s__UBA4372 sp902799985	77.0527	67	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.87	97.87	0.82	0.82	2	-
GCA_017379075.1	s__UBA4372 sp017379075	76.9627	78	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.81	95.71	0.83	0.83	3	-
GCA_017559845.1	s__UBA4372 sp017559845	76.8677	78	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394305.1	s__UBA4372 sp002394305	76.8527	56	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_017469525.1	s__UBA4372 sp017469525	76.7432	75	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.07	96.85	0.89	0.86	4	-
GCA_017619585.1	s__UBA4372 sp017619585	76.3911	69	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004559785.1	s__UBA4372 sp004559785	76.1623	50	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:27:41,172] [INFO] GTDB search result was written to GCA_018385095.1_ASM1838509v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:27:41,173] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:27:41,176] [INFO] DFAST_QC result json was written to GCA_018385095.1_ASM1838509v1_genomic.fna/dqc_result.json
[2023-06-19 03:27:41,177] [INFO] DFAST_QC completed!
[2023-06-19 03:27:41,177] [INFO] Total running time: 0h1m20s