[2023-06-18 22:05:27,184] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:05:27,187] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:05:27,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference
[2023-06-18 22:05:28,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:05:28,397] [INFO] Task started: Prodigal
[2023-06-18 22:05:28,398] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0340bc4-6b59-4b15-9b84-7c2fe0dc0ce0/GCA_018673155.1_ASM1867315v1_genomic.fna.gz | prodigal -d GCA_018673155.1_ASM1867315v1_genomic.fna/cds.fna -a GCA_018673155.1_ASM1867315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:05:34,987] [INFO] Task succeeded: Prodigal
[2023-06-18 22:05:34,987] [INFO] Task started: HMMsearch
[2023-06-18 22:05:34,987] [INFO] Running command: hmmsearch --tblout GCA_018673155.1_ASM1867315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference/reference_markers.hmm GCA_018673155.1_ASM1867315v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:05:35,238] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:05:35,241] [INFO] Found 6/6 markers.
[2023-06-18 22:05:35,272] [INFO] Query marker FASTA was written to GCA_018673155.1_ASM1867315v1_genomic.fna/markers.fasta
[2023-06-18 22:05:35,273] [INFO] Task started: Blastn
[2023-06-18 22:05:35,273] [INFO] Running command: blastn -query GCA_018673155.1_ASM1867315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference/reference_markers.fasta -out GCA_018673155.1_ASM1867315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:05:35,892] [INFO] Task succeeded: Blastn
[2023-06-18 22:05:35,899] [INFO] Selected 33 target genomes.
[2023-06-18 22:05:35,899] [INFO] Target genome list was writen to GCA_018673155.1_ASM1867315v1_genomic.fna/target_genomes.txt
[2023-06-18 22:05:35,900] [INFO] Task started: fastANI
[2023-06-18 22:05:35,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0340bc4-6b59-4b15-9b84-7c2fe0dc0ce0/GCA_018673155.1_ASM1867315v1_genomic.fna.gz --refList GCA_018673155.1_ASM1867315v1_genomic.fna/target_genomes.txt --output GCA_018673155.1_ASM1867315v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:05:54,938] [INFO] Task succeeded: fastANI
[2023-06-18 22:05:54,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:05:54,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:05:54,941] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:05:54,942] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:05:54,942] [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
--------------------------------------------------------------------------------
[2023-06-18 22:05:54,947] [INFO] DFAST Taxonomy check result was written to GCA_018673155.1_ASM1867315v1_genomic.fna/tc_result.tsv
[2023-06-18 22:05:54,948] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:05:54,948] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:05:54,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference/checkm_data
[2023-06-18 22:05:54,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:05:54,982] [INFO] Task started: CheckM
[2023-06-18 22:05:54,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018673155.1_ASM1867315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018673155.1_ASM1867315v1_genomic.fna/checkm_input GCA_018673155.1_ASM1867315v1_genomic.fna/checkm_result
[2023-06-18 22:06:20,505] [INFO] Task succeeded: CheckM
[2023-06-18 22:06:20,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:06:20,534] [INFO] ===== Completeness check finished =====
[2023-06-18 22:06:20,535] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:06:20,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018673155.1_ASM1867315v1_genomic.fna/markers.fasta)
[2023-06-18 22:06:20,535] [INFO] Task started: Blastn
[2023-06-18 22:06:20,536] [INFO] Running command: blastn -query GCA_018673155.1_ASM1867315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02c11af6-7d0c-427b-9f75-870feaf1a947/dqc_reference/reference_markers_gtdb.fasta -out GCA_018673155.1_ASM1867315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:06:21,375] [INFO] Task succeeded: Blastn
[2023-06-18 22:06:21,383] [INFO] Selected 21 target genomes.
[2023-06-18 22:06:21,383] [INFO] Target genome list was writen to GCA_018673155.1_ASM1867315v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:06:21,386] [INFO] Task started: fastANI
[2023-06-18 22:06:21,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0340bc4-6b59-4b15-9b84-7c2fe0dc0ce0/GCA_018673155.1_ASM1867315v1_genomic.fna.gz --refList GCA_018673155.1_ASM1867315v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018673155.1_ASM1867315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:06:29,378] [INFO] Task succeeded: fastANI
[2023-06-18 22:06:29,397] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:06:29,397] [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_000173095.1	s__MS024-2A sp000173095	99.5731	545	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	conclusive
GCA_905181895.1	s__MS024-2A sp905181895	80.4899	222	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	79.8149	368	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292265.1	s__MS024-2A sp002292265	78.8782	137	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_905182305.1	s__MS024-2A sp905182305	77.8953	244	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	77.8842	215	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_011525195.1	s__MS024-2A sp011525195	76.988	109	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699935.1	s__MS024-2A sp018699935	76.972	88	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	-
GCA_017851655.1	s__MS024-2A sp017851655	76.9363	152	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_017858055.1	s__MS024-2A sp002384715	76.8682	125	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_002167945.1	s__MS024-2A sp002167945	76.802	115	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517245.1	s__MS024-2A sp902517245	76.6862	73	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546725.1	s__MS024-2A sp902546725	76.5263	110	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	76.4873	74	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616905.1	s__MS024-2A sp902616905	76.4057	73	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857815.1	s__UBA8316 sp017857815	76.3958	64	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	76.3791	72	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCF_900105145.1	s__Polaribacter sp900105145	75.4298	52	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:06:29,401] [INFO] GTDB search result was written to GCA_018673155.1_ASM1867315v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:06:29,401] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:06:29,405] [INFO] DFAST_QC result json was written to GCA_018673155.1_ASM1867315v1_genomic.fna/dqc_result.json
[2023-06-18 22:06:29,405] [INFO] DFAST_QC completed!
[2023-06-18 22:06:29,405] [INFO] Total running time: 0h1m2s