[2023-03-18 03:59:27,752] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:27,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:27,753] [INFO] DQC Reference Directory: /var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference
[2023-03-18 03:59:29,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:29,369] [INFO] Task started: Prodigal
[2023-03-18 03:59:29,370] [INFO] Running command: cat /var/lib/cwl/stg3c7801ef-8d00-48c3-9707-5d87b86e4324/OceanDNA-b35009.fa | prodigal -d OceanDNA-b35009/cds.fna -a OceanDNA-b35009/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:51,435] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:51,436] [INFO] Task started: HMMsearch
[2023-03-18 03:59:51,436] [INFO] Running command: hmmsearch --tblout OceanDNA-b35009/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference/reference_markers.hmm OceanDNA-b35009/protein.faa > /dev/null
[2023-03-18 03:59:51,671] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:51,671] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c7801ef-8d00-48c3-9707-5d87b86e4324/OceanDNA-b35009.fa]
[2023-03-18 03:59:51,696] [INFO] Query marker FASTA was written to OceanDNA-b35009/markers.fasta
[2023-03-18 03:59:51,697] [INFO] Task started: Blastn
[2023-03-18 03:59:51,697] [INFO] Running command: blastn -query OceanDNA-b35009/markers.fasta -db /var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference/reference_markers.fasta -out OceanDNA-b35009/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:52,268] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:52,269] [INFO] Selected 11 target genomes.
[2023-03-18 03:59:52,269] [INFO] Target genome list was writen to OceanDNA-b35009/target_genomes.txt
[2023-03-18 03:59:52,275] [INFO] Task started: fastANI
[2023-03-18 03:59:52,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c7801ef-8d00-48c3-9707-5d87b86e4324/OceanDNA-b35009.fa --refList OceanDNA-b35009/target_genomes.txt --output OceanDNA-b35009/fastani_result.tsv --threads 1
[2023-03-18 04:00:02,987] [INFO] Task succeeded: fastANI
[2023-03-18 04:00:02,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:00:02,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:00:02,995] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 04:00:02,995] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-18 04:00:02,995] [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
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	98.7852	1302	1358	95	inconclusive
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	97.5438	1272	1358	95	inconclusive
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	93.806	1255	1358	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	86.2253	948	1358	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	83.3301	943	1358	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	83.3245	952	1358	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	79.1506	549	1358	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.9054	471	1358	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	77.5201	213	1358	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	76.0166	65	1358	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	75.9474	56	1358	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:00:02,995] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35009/tc_result.tsv
[2023-03-18 04:00:02,995] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:00:02,996] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:00:02,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference/checkm_data
[2023-03-18 04:00:02,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:00:03,002] [INFO] Task started: CheckM
[2023-03-18 04:00:03,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35009/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35009/checkm_input OceanDNA-b35009/checkm_result
[2023-03-18 04:00:57,991] [INFO] Task succeeded: CheckM
[2023-03-18 04:00:57,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:00:57,994] [INFO] ===== Completeness check finished =====
[2023-03-18 04:00:57,994] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:00:57,994] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35009/markers.fasta)
[2023-03-18 04:00:57,994] [INFO] Task started: Blastn
[2023-03-18 04:00:57,994] [INFO] Running command: blastn -query OceanDNA-b35009/markers.fasta -db /var/lib/cwl/stga88686aa-cbfa-4829-9d2e-3229832d655f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35009/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:00:58,782] [INFO] Task succeeded: Blastn
[2023-03-18 04:00:58,783] [INFO] Selected 9 target genomes.
[2023-03-18 04:00:58,783] [INFO] Target genome list was writen to OceanDNA-b35009/target_genomes_gtdb.txt
[2023-03-18 04:00:58,815] [INFO] Task started: fastANI
[2023-03-18 04:00:58,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c7801ef-8d00-48c3-9707-5d87b86e4324/OceanDNA-b35009.fa --refList OceanDNA-b35009/target_genomes_gtdb.txt --output OceanDNA-b35009/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:01:08,687] [INFO] Task succeeded: fastANI
[2023-03-18 04:01:08,693] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:01:08,694] [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_001641615.1	s__Pseudoalteromonas gelatinilytica	98.7852	1302	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	conclusive
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	93.806	1255	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	93.3461	1144	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	93.2913	1224	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	93.104	1213	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	92.4943	1164	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	90.4693	946	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	89.7306	1117	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	86.2012	951	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-18 04:01:08,694] [INFO] GTDB search result was written to OceanDNA-b35009/result_gtdb.tsv
[2023-03-18 04:01:08,694] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:01:08,695] [INFO] DFAST_QC result json was written to OceanDNA-b35009/dqc_result.json
[2023-03-18 04:01:08,695] [INFO] DFAST_QC completed!
[2023-03-18 04:01:08,695] [INFO] Total running time: 0h1m41s