[2023-03-18 03:28:30,806] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,806] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference
[2023-03-18 03:28:31,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,892] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,892] [INFO] Running command: cat /var/lib/cwl/stg465b36b4-18ed-4681-b886-546b369b2d0c/OceanDNA-b34305.fa | prodigal -d OceanDNA-b34305/cds.fna -a OceanDNA-b34305/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:55,264] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:55,264] [INFO] Task started: HMMsearch
[2023-03-18 03:28:55,264] [INFO] Running command: hmmsearch --tblout OceanDNA-b34305/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference/reference_markers.hmm OceanDNA-b34305/protein.faa > /dev/null
[2023-03-18 03:28:55,506] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:55,506] [INFO] Found 6/6 markers.
[2023-03-18 03:28:55,530] [INFO] Query marker FASTA was written to OceanDNA-b34305/markers.fasta
[2023-03-18 03:28:55,530] [INFO] Task started: Blastn
[2023-03-18 03:28:55,530] [INFO] Running command: blastn -query OceanDNA-b34305/markers.fasta -db /var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference/reference_markers.fasta -out OceanDNA-b34305/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:56,180] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:56,181] [INFO] Selected 18 target genomes.
[2023-03-18 03:28:56,181] [INFO] Target genome list was writen to OceanDNA-b34305/target_genomes.txt
[2023-03-18 03:28:56,191] [INFO] Task started: fastANI
[2023-03-18 03:28:56,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg465b36b4-18ed-4681-b886-546b369b2d0c/OceanDNA-b34305.fa --refList OceanDNA-b34305/target_genomes.txt --output OceanDNA-b34305/fastani_result.tsv --threads 1
[2023-03-18 03:29:09,996] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:09,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:29:09,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:29:10,004] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 03:29:10,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 03:29:10,004] [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 lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	99.5592	1335	1411	95	conclusive
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	92.9412	1199	1411	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	79.886	428	1411	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	79.014	366	1411	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.7637	350	1411	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.7536	377	1411	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.6184	376	1411	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.6104	378	1411	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.5967	327	1411	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.5794	294	1411	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:29:10,004] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34305/tc_result.tsv
[2023-03-18 03:29:10,004] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:29:10,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:29:10,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference/checkm_data
[2023-03-18 03:29:10,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:29:10,011] [INFO] Task started: CheckM
[2023-03-18 03:29:10,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34305/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34305/checkm_input OceanDNA-b34305/checkm_result
[2023-03-18 03:30:07,882] [INFO] Task succeeded: CheckM
[2023-03-18 03:30:07,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:30:07,885] [INFO] ===== Completeness check finished =====
[2023-03-18 03:30:07,885] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:30:07,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34305/markers.fasta)
[2023-03-18 03:30:07,886] [INFO] Task started: Blastn
[2023-03-18 03:30:07,886] [INFO] Running command: blastn -query OceanDNA-b34305/markers.fasta -db /var/lib/cwl/stg7de9cc88-ba49-4360-a08d-8eff1c7df84e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34305/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:30:08,887] [INFO] Task succeeded: Blastn
[2023-03-18 03:30:08,888] [INFO] Selected 8 target genomes.
[2023-03-18 03:30:08,888] [INFO] Target genome list was writen to OceanDNA-b34305/target_genomes_gtdb.txt
[2023-03-18 03:30:08,894] [INFO] Task started: fastANI
[2023-03-18 03:30:08,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg465b36b4-18ed-4681-b886-546b369b2d0c/OceanDNA-b34305.fa --refList OceanDNA-b34305/target_genomes_gtdb.txt --output OceanDNA-b34305/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:30:16,453] [INFO] Task succeeded: fastANI
[2023-03-18 03:30:16,458] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:30:16,458] [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_902506055.1	s__Alteromonas lipotrueae	99.5332	1348	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	conclusive
GCF_000213655.1	s__Alteromonas naphthalenivorans	92.9412	1199	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_018100795.1	s__Alteromonas sp018100795	89.779	1199	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001562115.1	s__Alteromonas stellipolaris	89.6352	1255	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_000730385.1	s__Alteromonas australica	79.8769	430	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_010500865.1	s__Alteromonas profundi	79.0264	365	1411	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	78.7732	348	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_016405965.1	s__Alteromonas sp016405965	78.5633	369	1411	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 03:30:16,458] [INFO] GTDB search result was written to OceanDNA-b34305/result_gtdb.tsv
[2023-03-18 03:30:16,458] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:30:16,460] [INFO] DFAST_QC result json was written to OceanDNA-b34305/dqc_result.json
[2023-03-18 03:30:16,460] [INFO] DFAST_QC completed!
[2023-03-18 03:30:16,460] [INFO] Total running time: 0h1m46s