[2023-03-16 17:15:23,145] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:15:23,145] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:15:23,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference
[2023-03-16 17:15:24,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:15:24,277] [INFO] Task started: Prodigal
[2023-03-16 17:15:24,277] [INFO] Running command: cat /var/lib/cwl/stgcc62c1bf-2dbd-4e3c-96b6-23a6d544814b/OceanDNA-b35143.fa | prodigal -d OceanDNA-b35143/cds.fna -a OceanDNA-b35143/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:15:42,917] [INFO] Task succeeded: Prodigal
[2023-03-16 17:15:42,917] [INFO] Task started: HMMsearch
[2023-03-16 17:15:42,917] [INFO] Running command: hmmsearch --tblout OceanDNA-b35143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference/reference_markers.hmm OceanDNA-b35143/protein.faa > /dev/null
[2023-03-16 17:15:43,137] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:15:43,138] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcc62c1bf-2dbd-4e3c-96b6-23a6d544814b/OceanDNA-b35143.fa]
[2023-03-16 17:15:43,158] [INFO] Query marker FASTA was written to OceanDNA-b35143/markers.fasta
[2023-03-16 17:15:43,159] [INFO] Task started: Blastn
[2023-03-16 17:15:43,159] [INFO] Running command: blastn -query OceanDNA-b35143/markers.fasta -db /var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference/reference_markers.fasta -out OceanDNA-b35143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:15:43,826] [INFO] Task succeeded: Blastn
[2023-03-16 17:15:43,827] [INFO] Selected 21 target genomes.
[2023-03-16 17:15:43,827] [INFO] Target genome list was writen to OceanDNA-b35143/target_genomes.txt
[2023-03-16 17:15:43,839] [INFO] Task started: fastANI
[2023-03-16 17:15:43,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc62c1bf-2dbd-4e3c-96b6-23a6d544814b/OceanDNA-b35143.fa --refList OceanDNA-b35143/target_genomes.txt --output OceanDNA-b35143/fastani_result.tsv --threads 1
[2023-03-16 17:15:57,259] [INFO] Task succeeded: fastANI
[2023-03-16 17:15:57,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:15:57,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:15:57,268] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:15:57,268] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:15:57,268] [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
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	79.0014	259	1080	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.9684	338	1080	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.6337	249	1080	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	78.4617	256	1080	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.3199	143	1080	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.2572	100	1080	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.0431	146	1080	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.0331	190	1080	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.8636	181	1080	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.8535	136	1080	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	77.7492	149	1080	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	77.1427	80	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:15:57,269] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35143/tc_result.tsv
[2023-03-16 17:15:57,269] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:15:57,269] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:15:57,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference/checkm_data
[2023-03-16 17:15:57,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:15:57,274] [INFO] Task started: CheckM
[2023-03-16 17:15:57,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35143/checkm_input OceanDNA-b35143/checkm_result
[2023-03-16 17:17:04,529] [INFO] Task succeeded: CheckM
[2023-03-16 17:17:04,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:17:04,533] [INFO] ===== Completeness check finished =====
[2023-03-16 17:17:04,533] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:17:04,533] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35143/markers.fasta)
[2023-03-16 17:17:04,535] [INFO] Task started: Blastn
[2023-03-16 17:17:04,535] [INFO] Running command: blastn -query OceanDNA-b35143/markers.fasta -db /var/lib/cwl/stg0d31565f-527f-4892-8197-4940d16b233e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:17:07,646] [INFO] Task succeeded: Blastn
[2023-03-16 17:17:07,649] [INFO] Selected 14 target genomes.
[2023-03-16 17:17:07,649] [INFO] Target genome list was writen to OceanDNA-b35143/target_genomes_gtdb.txt
[2023-03-16 17:17:07,657] [INFO] Task started: fastANI
[2023-03-16 17:17:07,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc62c1bf-2dbd-4e3c-96b6-23a6d544814b/OceanDNA-b35143.fa --refList OceanDNA-b35143/target_genomes_gtdb.txt --output OceanDNA-b35143/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:17:19,543] [INFO] Task succeeded: fastANI
[2023-03-16 17:17:19,550] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:17:19,550] [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_015644725.1	s__Alteromonas sp015644725	87.5291	913	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249245.1	s__Alteromonas lipotrueiana	80.7136	595	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	79.6783	438	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_005222225.1	s__Alteromonas lutimaris	78.9684	338	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228385.1	s__Alteromonas iocasae	78.6558	247	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	78.4533	256	1080	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	78.3199	143	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651815.1	s__Alteromonas halophila	78.0263	191	1080	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	77.7429	150	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	77.7414	114	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_000753865.1	s__Alteromonas sp000753865	77.5203	110	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014645355.1	s__Bowmanella pacifica	77.1126	81	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:17:19,551] [INFO] GTDB search result was written to OceanDNA-b35143/result_gtdb.tsv
[2023-03-16 17:17:19,551] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:17:19,553] [INFO] DFAST_QC result json was written to OceanDNA-b35143/dqc_result.json
[2023-03-16 17:17:19,553] [INFO] DFAST_QC completed!
[2023-03-16 17:17:19,553] [INFO] Total running time: 0h1m56s