[2023-03-15 22:25:05,844] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:25:05,844] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:25:05,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference
[2023-03-15 22:25:06,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:25:06,963] [INFO] Task started: Prodigal
[2023-03-15 22:25:06,963] [INFO] Running command: cat /var/lib/cwl/stgf31c5bcf-d98a-40ed-b638-c283c36a888c/OceanDNA-b34562.fa | prodigal -d OceanDNA-b34562/cds.fna -a OceanDNA-b34562/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:25:25,554] [INFO] Task succeeded: Prodigal
[2023-03-15 22:25:25,554] [INFO] Task started: HMMsearch
[2023-03-15 22:25:25,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b34562/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference/reference_markers.hmm OceanDNA-b34562/protein.faa > /dev/null
[2023-03-15 22:25:25,772] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:25:25,772] [INFO] Found 6/6 markers.
[2023-03-15 22:25:25,792] [INFO] Query marker FASTA was written to OceanDNA-b34562/markers.fasta
[2023-03-15 22:25:25,793] [INFO] Task started: Blastn
[2023-03-15 22:25:25,793] [INFO] Running command: blastn -query OceanDNA-b34562/markers.fasta -db /var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference/reference_markers.fasta -out OceanDNA-b34562/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:26,434] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:26,435] [INFO] Selected 22 target genomes.
[2023-03-15 22:25:26,435] [INFO] Target genome list was writen to OceanDNA-b34562/target_genomes.txt
[2023-03-15 22:25:26,448] [INFO] Task started: fastANI
[2023-03-15 22:25:26,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgf31c5bcf-d98a-40ed-b638-c283c36a888c/OceanDNA-b34562.fa --refList OceanDNA-b34562/target_genomes.txt --output OceanDNA-b34562/fastani_result.tsv --threads 1
[2023-03-15 22:25:41,905] [INFO] Task succeeded: fastANI
[2023-03-15 22:25:41,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:25:41,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:25:41,912] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 22:25:41,913] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 22:25:41,913] [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 genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	98.2161	987	1112	95	conclusive
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	81.9987	609	1112	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	79.2126	349	1112	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	79.0988	344	1112	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.0419	347	1112	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	79.0393	348	1112	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.9746	351	1112	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.2899	115	1112	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.7598	97	1112	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	77.333	91	1112	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:25:41,913] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34562/tc_result.tsv
[2023-03-15 22:25:41,913] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:25:41,913] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:25:41,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference/checkm_data
[2023-03-15 22:25:41,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:25:42,044] [INFO] Task started: CheckM
[2023-03-15 22:25:42,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34562/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34562/checkm_input OceanDNA-b34562/checkm_result
[2023-03-15 22:26:29,731] [INFO] Task succeeded: CheckM
[2023-03-15 22:26:29,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:26:29,735] [INFO] ===== Completeness check finished =====
[2023-03-15 22:26:29,735] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:26:29,735] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34562/markers.fasta)
[2023-03-15 22:26:29,736] [INFO] Task started: Blastn
[2023-03-15 22:26:29,736] [INFO] Running command: blastn -query OceanDNA-b34562/markers.fasta -db /var/lib/cwl/stgba1be2ef-e638-4177-a305-a48aaf7a150d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34562/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:26:30,756] [INFO] Task succeeded: Blastn
[2023-03-15 22:26:30,757] [INFO] Selected 15 target genomes.
[2023-03-15 22:26:30,757] [INFO] Target genome list was writen to OceanDNA-b34562/target_genomes_gtdb.txt
[2023-03-15 22:26:30,784] [INFO] Task started: fastANI
[2023-03-15 22:26:30,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgf31c5bcf-d98a-40ed-b638-c283c36a888c/OceanDNA-b34562.fa --refList OceanDNA-b34562/target_genomes_gtdb.txt --output OceanDNA-b34562/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:26:42,611] [INFO] Task succeeded: fastANI
[2023-03-15 22:26:42,619] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:26:42,619] [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_010500895.1	s__Alteromonas genovensis	98.2161	987	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	conclusive
GCF_000753865.1	s__Alteromonas sp000753865	94.2069	993	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002691625.1	s__Alteromonas sp002691625	83.4273	85	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_010500915.1	s__Alteromonas hispanica	82.0149	609	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCF_903772925.1	s__Alteromonas macleodii_A	79.2331	338	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005117025.1	s__Alteromonas portus	79.2254	348	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000597705.1	s__Alteromonas sp000597705	79.1153	328	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_002993325.1	s__Alteromonas gracilis	79.0367	347	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_000172635.2	s__Alteromonas macleodii	78.9873	350	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_001885075.1	s__Alteromonas sp001885075	78.9353	300	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756315.1	s__Alteromonas sp009811495	78.8114	322	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_000730385.1	s__Alteromonas australica	78.4185	265	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_006538345.1	s__Alteromonas sp006538345	77.7661	151	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:26:42,619] [INFO] GTDB search result was written to OceanDNA-b34562/result_gtdb.tsv
[2023-03-15 22:26:42,619] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:26:42,621] [INFO] DFAST_QC result json was written to OceanDNA-b34562/dqc_result.json
[2023-03-15 22:26:42,621] [INFO] DFAST_QC completed!
[2023-03-15 22:26:42,621] [INFO] Total running time: 0h1m37s