[2023-03-16 09:43:37,170] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,170] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,170] [INFO] DQC Reference Directory: /var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference
[2023-03-16 09:43:39,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,239] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,239] [INFO] Running command: cat /var/lib/cwl/stgb44b2acb-27ec-40b7-a60b-e04ebdafa3d4/OceanDNA-b7487.fa | prodigal -d OceanDNA-b7487/cds.fna -a OceanDNA-b7487/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:44:06,704] [INFO] Task succeeded: Prodigal
[2023-03-16 09:44:06,704] [INFO] Task started: HMMsearch
[2023-03-16 09:44:06,704] [INFO] Running command: hmmsearch --tblout OceanDNA-b7487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference/reference_markers.hmm OceanDNA-b7487/protein.faa > /dev/null
[2023-03-16 09:44:06,922] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:44:06,923] [INFO] Found 6/6 markers.
[2023-03-16 09:44:06,948] [INFO] Query marker FASTA was written to OceanDNA-b7487/markers.fasta
[2023-03-16 09:44:06,949] [INFO] Task started: Blastn
[2023-03-16 09:44:06,949] [INFO] Running command: blastn -query OceanDNA-b7487/markers.fasta -db /var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference/reference_markers.fasta -out OceanDNA-b7487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:07,539] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:07,540] [INFO] Selected 13 target genomes.
[2023-03-16 09:44:07,540] [INFO] Target genome list was writen to OceanDNA-b7487/target_genomes.txt
[2023-03-16 09:44:07,706] [INFO] Task started: fastANI
[2023-03-16 09:44:07,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgb44b2acb-27ec-40b7-a60b-e04ebdafa3d4/OceanDNA-b7487.fa --refList OceanDNA-b7487/target_genomes.txt --output OceanDNA-b7487/fastani_result.tsv --threads 1
[2023-03-16 09:44:18,492] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:18,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:44:18,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:44:18,500] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:44:18,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:44:18,501] [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
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	84.4832	871	1373	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	83.3247	844	1373	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	83.2937	956	1373	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	83.2807	952	1373	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	83.2411	863	1373	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	83.013	903	1373	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	79.752	454	1373	95	below_threshold
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	79.73	536	1373	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.8609	85	1373	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.7019	67	1373	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.5067	57	1373	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.8188	65	1373	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	75.6582	70	1373	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:44:18,501] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7487/tc_result.tsv
[2023-03-16 09:44:18,501] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:44:18,501] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:44:18,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference/checkm_data
[2023-03-16 09:44:18,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:44:18,507] [INFO] Task started: CheckM
[2023-03-16 09:44:18,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7487/checkm_input OceanDNA-b7487/checkm_result
[2023-03-16 09:45:26,002] [INFO] Task succeeded: CheckM
[2023-03-16 09:45:26,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:45:26,072] [INFO] ===== Completeness check finished =====
[2023-03-16 09:45:26,073] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:45:26,073] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7487/markers.fasta)
[2023-03-16 09:45:26,074] [INFO] Task started: Blastn
[2023-03-16 09:45:26,074] [INFO] Running command: blastn -query OceanDNA-b7487/markers.fasta -db /var/lib/cwl/stg3884523d-a8e5-40d7-b801-f71f87aa67c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:45:26,927] [INFO] Task succeeded: Blastn
[2023-03-16 09:45:26,947] [INFO] Selected 7 target genomes.
[2023-03-16 09:45:26,947] [INFO] Target genome list was writen to OceanDNA-b7487/target_genomes_gtdb.txt
[2023-03-16 09:45:26,952] [INFO] Task started: fastANI
[2023-03-16 09:45:26,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgb44b2acb-27ec-40b7-a60b-e04ebdafa3d4/OceanDNA-b7487.fa --refList OceanDNA-b7487/target_genomes_gtdb.txt --output OceanDNA-b7487/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:45:33,665] [INFO] Task succeeded: fastANI
[2023-03-16 09:45:33,671] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:45:33,671] [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
GCF_000152985.1	s__Leeuwenhoekiella blandensis	84.4832	871	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	83.5981	969	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	83.2963	956	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	83.2412	863	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	83.006	904	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	79.7277	537	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	79.5305	580	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:45:33,676] [INFO] GTDB search result was written to OceanDNA-b7487/result_gtdb.tsv
[2023-03-16 09:45:33,681] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:45:33,687] [INFO] DFAST_QC result json was written to OceanDNA-b7487/dqc_result.json
[2023-03-16 09:45:33,688] [INFO] DFAST_QC completed!
[2023-03-16 09:45:33,688] [INFO] Total running time: 0h1m57s