[2023-03-17 07:47:46,523] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,523] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,523] [INFO] DQC Reference Directory: /var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference
[2023-03-17 07:47:47,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,625] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,625] [INFO] Running command: cat /var/lib/cwl/stga5c6c894-dfd6-4b8d-81c5-762dfb417d8d/OceanDNA-b34330.fa | prodigal -d OceanDNA-b34330/cds.fna -a OceanDNA-b34330/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:48:10,437] [INFO] Task succeeded: Prodigal
[2023-03-17 07:48:10,438] [INFO] Task started: HMMsearch
[2023-03-17 07:48:10,438] [INFO] Running command: hmmsearch --tblout OceanDNA-b34330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference/reference_markers.hmm OceanDNA-b34330/protein.faa > /dev/null
[2023-03-17 07:48:10,657] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:48:10,658] [INFO] Found 6/6 markers.
[2023-03-17 07:48:10,682] [INFO] Query marker FASTA was written to OceanDNA-b34330/markers.fasta
[2023-03-17 07:48:10,682] [INFO] Task started: Blastn
[2023-03-17 07:48:10,682] [INFO] Running command: blastn -query OceanDNA-b34330/markers.fasta -db /var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference/reference_markers.fasta -out OceanDNA-b34330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:11,332] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:11,333] [INFO] Selected 13 target genomes.
[2023-03-17 07:48:11,333] [INFO] Target genome list was writen to OceanDNA-b34330/target_genomes.txt
[2023-03-17 07:48:11,341] [INFO] Task started: fastANI
[2023-03-17 07:48:11,341] [INFO] Running command: fastANI --query /var/lib/cwl/stga5c6c894-dfd6-4b8d-81c5-762dfb417d8d/OceanDNA-b34330.fa --refList OceanDNA-b34330/target_genomes.txt --output OceanDNA-b34330/fastani_result.tsv --threads 1
[2023-03-17 07:48:21,013] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:21,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:48:21,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:48:21,019] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 07:48:21,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 07:48:21,020] [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
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	98.7079	1241	1346	95	conclusive
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	81.3731	504	1346	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	80.9527	413	1346	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	80.1411	384	1346	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	80.1108	401	1346	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	80.0945	390	1346	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.9389	387	1346	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	79.4575	426	1346	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:48:21,020] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34330/tc_result.tsv
[2023-03-17 07:48:21,020] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:48:21,020] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:48:21,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference/checkm_data
[2023-03-17 07:48:21,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:48:21,026] [INFO] Task started: CheckM
[2023-03-17 07:48:21,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34330/checkm_input OceanDNA-b34330/checkm_result
[2023-03-17 07:49:17,568] [INFO] Task succeeded: CheckM
[2023-03-17 07:49:17,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:49:17,571] [INFO] ===== Completeness check finished =====
[2023-03-17 07:49:17,571] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:49:17,572] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34330/markers.fasta)
[2023-03-17 07:49:17,572] [INFO] Task started: Blastn
[2023-03-17 07:49:17,572] [INFO] Running command: blastn -query OceanDNA-b34330/markers.fasta -db /var/lib/cwl/stge8c7af21-89a5-4d0d-842f-148d2d451528/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:49:18,594] [INFO] Task succeeded: Blastn
[2023-03-17 07:49:18,595] [INFO] Selected 18 target genomes.
[2023-03-17 07:49:18,595] [INFO] Target genome list was writen to OceanDNA-b34330/target_genomes_gtdb.txt
[2023-03-17 07:49:18,721] [INFO] Task started: fastANI
[2023-03-17 07:49:18,721] [INFO] Running command: fastANI --query /var/lib/cwl/stga5c6c894-dfd6-4b8d-81c5-762dfb417d8d/OceanDNA-b34330.fa --refList OceanDNA-b34330/target_genomes_gtdb.txt --output OceanDNA-b34330/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:49:32,815] [INFO] Task succeeded: fastANI
[2023-03-17 07:49:32,825] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:49:32,825] [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_000730385.1	s__Alteromonas australica	98.7079	1241	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	conclusive
GCF_010500865.1	s__Alteromonas profundi	81.3655	504	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020585.3	s__Alteromonas mediterranea	80.9886	412	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_016405965.1	s__Alteromonas sp016405965	80.5741	369	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	80.1324	384	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_005117025.1	s__Alteromonas portus	80.1107	401	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	80.1091	389	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_000597705.1	s__Alteromonas sp000597705	80.0998	403	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_903772925.1	s__Alteromonas macleodii_A	80.0608	428	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	79.947	387	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_016756315.1	s__Alteromonas sp009811495	79.9421	357	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_003443615.1	s__Alteromonas sp003443615	79.88	414	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000808575.1	s__Alteromonas marina	79.793	421	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_009811415.1	s__Alteromonas sp009811415	79.741	370	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	79.6587	442	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	79.445	429	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_010500895.1	s__Alteromonas genovensis	79.1251	314	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	-
GCF_000753865.1	s__Alteromonas sp000753865	79.0186	331	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 07:49:32,826] [INFO] GTDB search result was written to OceanDNA-b34330/result_gtdb.tsv
[2023-03-17 07:49:32,826] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:49:32,827] [INFO] DFAST_QC result json was written to OceanDNA-b34330/dqc_result.json
[2023-03-17 07:49:32,827] [INFO] DFAST_QC completed!
[2023-03-17 07:49:32,827] [INFO] Total running time: 0h1m46s