[2023-03-18 06:30:24,689] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,689] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference
[2023-03-18 06:30:25,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,871] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,871] [INFO] Running command: cat /var/lib/cwl/stg1fb6d7f4-cc38-4f0e-95fb-4d945d68c71b/OceanDNA-b34288.fa | prodigal -d OceanDNA-b34288/cds.fna -a OceanDNA-b34288/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:53,585] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:53,585] [INFO] Task started: HMMsearch
[2023-03-18 06:30:53,585] [INFO] Running command: hmmsearch --tblout OceanDNA-b34288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference/reference_markers.hmm OceanDNA-b34288/protein.faa > /dev/null
[2023-03-18 06:30:53,827] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:53,828] [INFO] Found 6/6 markers.
[2023-03-18 06:30:53,874] [INFO] Query marker FASTA was written to OceanDNA-b34288/markers.fasta
[2023-03-18 06:30:53,875] [INFO] Task started: Blastn
[2023-03-18 06:30:53,875] [INFO] Running command: blastn -query OceanDNA-b34288/markers.fasta -db /var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference/reference_markers.fasta -out OceanDNA-b34288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:54,538] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:54,548] [INFO] Selected 23 target genomes.
[2023-03-18 06:30:54,548] [INFO] Target genome list was writen to OceanDNA-b34288/target_genomes.txt
[2023-03-18 06:30:54,570] [INFO] Task started: fastANI
[2023-03-18 06:30:54,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fb6d7f4-cc38-4f0e-95fb-4d945d68c71b/OceanDNA-b34288.fa --refList OceanDNA-b34288/target_genomes.txt --output OceanDNA-b34288/fastani_result.tsv --threads 1
[2023-03-18 06:31:10,347] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:10,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:31:10,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:31:10,357] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:31:10,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:31:10,357] [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 alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.9841	421	1570	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	78.7271	421	1570	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.5785	367	1570	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	78.5224	377	1570	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	77.4092	142	1570	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	77.3469	128	1570	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	77.1972	209	1570	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	77.1435	144	1570	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	77.0752	141	1570	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	76.9657	179	1570	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	76.9002	135	1570	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	76.8713	162	1570	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	76.4505	120	1570	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	75.9718	56	1570	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:31:10,360] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34288/tc_result.tsv
[2023-03-18 06:31:10,365] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:31:10,365] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:31:10,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference/checkm_data
[2023-03-18 06:31:10,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:31:10,383] [INFO] Task started: CheckM
[2023-03-18 06:31:10,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34288/checkm_input OceanDNA-b34288/checkm_result
[2023-03-18 06:32:18,460] [INFO] Task succeeded: CheckM
[2023-03-18 06:32:18,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:32:18,567] [INFO] ===== Completeness check finished =====
[2023-03-18 06:32:18,567] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:32:18,567] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34288/markers.fasta)
[2023-03-18 06:32:18,568] [INFO] Task started: Blastn
[2023-03-18 06:32:18,568] [INFO] Running command: blastn -query OceanDNA-b34288/markers.fasta -db /var/lib/cwl/stgda2be6dd-b9f1-4621-bbde-028da7ec7e7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:32:19,728] [INFO] Task succeeded: Blastn
[2023-03-18 06:32:19,732] [INFO] Selected 12 target genomes.
[2023-03-18 06:32:19,733] [INFO] Target genome list was writen to OceanDNA-b34288/target_genomes_gtdb.txt
[2023-03-18 06:32:19,914] [INFO] Task started: fastANI
[2023-03-18 06:32:19,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fb6d7f4-cc38-4f0e-95fb-4d945d68c71b/OceanDNA-b34288.fa --refList OceanDNA-b34288/target_genomes_gtdb.txt --output OceanDNA-b34288/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:32:30,596] [INFO] Task succeeded: fastANI
[2023-03-18 06:32:30,604] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:32:30,604] [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_900129565.1	s__Alteromonas aggregata	98.0381	1469	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	conclusive
GCA_017794925.1	s__Alteromonas sp017794925	86.7558	1103	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494365.1	s__Alteromonas mangrovi	82.3353	959	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	78.9918	419	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222405.1	s__Alteromonas sp018222405	78.9686	443	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	78.7425	420	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	78.6439	391	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_001758465.1	s__Alteromonas lipolytica	78.5898	366	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013373625.1	s__Alteromonas sp013373625	77.8536	298	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	77.4517	199	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_000020585.3	s__Alteromonas mediterranea	77.3548	127	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_005222225.1	s__Alteromonas lutimaris	76.9012	159	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:32:30,607] [INFO] GTDB search result was written to OceanDNA-b34288/result_gtdb.tsv
[2023-03-18 06:32:30,607] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:32:30,611] [INFO] DFAST_QC result json was written to OceanDNA-b34288/dqc_result.json
[2023-03-18 06:32:30,611] [INFO] DFAST_QC completed!
[2023-03-18 06:32:30,611] [INFO] Total running time: 0h2m6s