[2023-06-28 08:21:38,666] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:21:38,668] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:21:38,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference
[2023-06-28 08:21:40,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:21:40,250] [INFO] Task started: Prodigal
[2023-06-28 08:21:40,250] [INFO] Running command: gunzip -c /var/lib/cwl/stgaee58d71-6162-4a8f-bd54-e551193542b2/GCA_017478035.1_ASM1747803v1_genomic.fna.gz | prodigal -d GCA_017478035.1_ASM1747803v1_genomic.fna/cds.fna -a GCA_017478035.1_ASM1747803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:21:51,348] [INFO] Task succeeded: Prodigal
[2023-06-28 08:21:51,349] [INFO] Task started: HMMsearch
[2023-06-28 08:21:51,349] [INFO] Running command: hmmsearch --tblout GCA_017478035.1_ASM1747803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference/reference_markers.hmm GCA_017478035.1_ASM1747803v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:21:51,601] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:21:51,603] [INFO] Found 6/6 markers.
[2023-06-28 08:21:51,627] [INFO] Query marker FASTA was written to GCA_017478035.1_ASM1747803v1_genomic.fna/markers.fasta
[2023-06-28 08:21:51,628] [INFO] Task started: Blastn
[2023-06-28 08:21:51,628] [INFO] Running command: blastn -query GCA_017478035.1_ASM1747803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference/reference_markers.fasta -out GCA_017478035.1_ASM1747803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:21:52,217] [INFO] Task succeeded: Blastn
[2023-06-28 08:21:52,222] [INFO] Selected 24 target genomes.
[2023-06-28 08:21:52,223] [INFO] Target genome list was writen to GCA_017478035.1_ASM1747803v1_genomic.fna/target_genomes.txt
[2023-06-28 08:21:52,225] [INFO] Task started: fastANI
[2023-06-28 08:21:52,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee58d71-6162-4a8f-bd54-e551193542b2/GCA_017478035.1_ASM1747803v1_genomic.fna.gz --refList GCA_017478035.1_ASM1747803v1_genomic.fna/target_genomes.txt --output GCA_017478035.1_ASM1747803v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:22:04,606] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:04,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:22:04,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:22:04,609] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:22:04,609] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:22:04,609] [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 08:22:04,611] [INFO] DFAST Taxonomy check result was written to GCA_017478035.1_ASM1747803v1_genomic.fna/tc_result.tsv
[2023-06-28 08:22:04,612] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:22:04,612] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:22:04,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference/checkm_data
[2023-06-28 08:22:04,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:22:04,643] [INFO] Task started: CheckM
[2023-06-28 08:22:04,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017478035.1_ASM1747803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017478035.1_ASM1747803v1_genomic.fna/checkm_input GCA_017478035.1_ASM1747803v1_genomic.fna/checkm_result
[2023-06-28 08:22:40,703] [INFO] Task succeeded: CheckM
[2023-06-28 08:22:40,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 08:22:40,724] [INFO] ===== Completeness check finished =====
[2023-06-28 08:22:40,725] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:22:40,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017478035.1_ASM1747803v1_genomic.fna/markers.fasta)
[2023-06-28 08:22:40,725] [INFO] Task started: Blastn
[2023-06-28 08:22:40,726] [INFO] Running command: blastn -query GCA_017478035.1_ASM1747803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3745514d-51e5-4b8f-a037-17f60885ba5d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017478035.1_ASM1747803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:22:41,534] [INFO] Task succeeded: Blastn
[2023-06-28 08:22:41,539] [INFO] Selected 23 target genomes.
[2023-06-28 08:22:41,539] [INFO] Target genome list was writen to GCA_017478035.1_ASM1747803v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:22:41,546] [INFO] Task started: fastANI
[2023-06-28 08:22:41,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee58d71-6162-4a8f-bd54-e551193542b2/GCA_017478035.1_ASM1747803v1_genomic.fna.gz --refList GCA_017478035.1_ASM1747803v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017478035.1_ASM1747803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:22:50,540] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:50,562] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:22:50,563] [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_017478035.1	s__RF16 sp017478035	100.0	582	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017447875.1	s__RF16 sp017447875	80.1716	219	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762355.1	s__RF16 sp902762355	80.0296	227	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799705.1	s__RF16 sp902799705	79.9661	263	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319105.1	s__RF16 sp900319105	79.9389	267	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.16	95.90	0.87	0.77	5	-
GCA_902780235.1	s__RF16 sp902780235	79.8868	220	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.20	95.41	0.81	0.78	4	-
GCA_902799875.1	s__RF16 sp902799875	79.832	208	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318245.1	s__RF16 sp900318245	79.7941	260	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.37	96.49	0.89	0.84	5	-
GCA_900321005.1	s__RF16 sp900321005	79.7111	227	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.51	96.64	0.88	0.83	5	-
GCA_902798015.1	s__RF16 sp902798015	79.6571	215	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769535.1	s__RF16 sp902769535	79.518	221	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320865.1	s__RF16 sp900320865	79.4882	207	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.08	95.30	0.82	0.79	13	-
GCA_900317885.1	s__RF16 sp900317885	79.4754	212	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.25	96.25	0.86	0.83	5	-
GCA_902799555.1	s__RF16 sp902799555	79.4545	229	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.18	96.01	0.81	0.78	3	-
GCA_017507715.1	s__RF16 sp017507715	79.4486	216	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317345.1	s__RF16 sp900317345	79.3489	189	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.36	96.72	0.91	0.83	3	-
GCA_017541805.1	s__RF16 sp017541805	79.3403	211	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233255.1	s__RF16 sp905233255	79.2885	228	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002351925.1	s__RF16 sp002351925	79.2327	212	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017446455.1	s__RF16 sp017446455	79.225	228	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800215.1	s__RF16 sp902800215	79.1025	196	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.87	96.87	0.85	0.85	2	-
GCA_017401985.1	s__RF16 sp017401985	78.8294	201	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017423085.1	s__RF16 sp017423085	78.5871	156	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.54	98.52	0.72	0.68	3	-
--------------------------------------------------------------------------------
[2023-06-28 08:22:50,565] [INFO] GTDB search result was written to GCA_017478035.1_ASM1747803v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:22:50,565] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:22:50,569] [INFO] DFAST_QC result json was written to GCA_017478035.1_ASM1747803v1_genomic.fna/dqc_result.json
[2023-06-28 08:22:50,569] [INFO] DFAST_QC completed!
[2023-06-28 08:22:50,569] [INFO] Total running time: 0h1m12s