[2023-03-17 05:34:58,126] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,126] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference
[2023-03-17 05:34:59,273] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,274] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,274] [INFO] Running command: cat /var/lib/cwl/stge26a0514-04a1-4d6d-ba43-0c9674266874/OceanDNA-b35091.fa | prodigal -d OceanDNA-b35091/cds.fna -a OceanDNA-b35091/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:19,391] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:19,392] [INFO] Task started: HMMsearch
[2023-03-17 05:35:19,392] [INFO] Running command: hmmsearch --tblout OceanDNA-b35091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference/reference_markers.hmm OceanDNA-b35091/protein.faa > /dev/null
[2023-03-17 05:35:19,638] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:19,638] [INFO] Found 6/6 markers.
[2023-03-17 05:35:19,686] [INFO] Query marker FASTA was written to OceanDNA-b35091/markers.fasta
[2023-03-17 05:35:19,687] [INFO] Task started: Blastn
[2023-03-17 05:35:19,687] [INFO] Running command: blastn -query OceanDNA-b35091/markers.fasta -db /var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference/reference_markers.fasta -out OceanDNA-b35091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:20,347] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:20,353] [INFO] Selected 13 target genomes.
[2023-03-17 05:35:20,353] [INFO] Target genome list was writen to OceanDNA-b35091/target_genomes.txt
[2023-03-17 05:35:20,361] [INFO] Task started: fastANI
[2023-03-17 05:35:20,361] [INFO] Running command: fastANI --query /var/lib/cwl/stge26a0514-04a1-4d6d-ba43-0c9674266874/OceanDNA-b35091.fa --refList OceanDNA-b35091/target_genomes.txt --output OceanDNA-b35091/fastani_result.tsv --threads 1
[2023-03-17 05:35:32,126] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:32,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:32,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:32,134] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2023-03-17 05:35:32,134] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-17 05:35:32,134] [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 tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	98.9016	1179	1266	95	inconclusive
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	98.8886	1154	1266	95	inconclusive
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	98.3711	1162	1266	95	inconclusive
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	98.3692	1160	1266	95	inconclusive
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	90.4328	1099	1266	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	81.1793	732	1266	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	81.1494	705	1266	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	81.1156	733	1266	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	81.0535	740	1266	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	75.8133	63	1266	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	75.4685	58	1266	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	75.4398	57	1266	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:35:32,136] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35091/tc_result.tsv
[2023-03-17 05:35:32,136] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:32,136] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:32,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference/checkm_data
[2023-03-17 05:35:32,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:32,190] [INFO] Task started: CheckM
[2023-03-17 05:35:32,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35091/checkm_input OceanDNA-b35091/checkm_result
[2023-03-17 05:36:23,096] [INFO] Task succeeded: CheckM
[2023-03-17 05:36:23,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:36:23,130] [INFO] ===== Completeness check finished =====
[2023-03-17 05:36:23,130] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:36:23,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35091/markers.fasta)
[2023-03-17 05:36:23,131] [INFO] Task started: Blastn
[2023-03-17 05:36:23,131] [INFO] Running command: blastn -query OceanDNA-b35091/markers.fasta -db /var/lib/cwl/stg91795dbd-02dd-4d39-8ff0-45107a2dbc7c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:36:24,175] [INFO] Task succeeded: Blastn
[2023-03-17 05:36:24,190] [INFO] Selected 12 target genomes.
[2023-03-17 05:36:24,190] [INFO] Target genome list was writen to OceanDNA-b35091/target_genomes_gtdb.txt
[2023-03-17 05:36:24,301] [INFO] Task started: fastANI
[2023-03-17 05:36:24,301] [INFO] Running command: fastANI --query /var/lib/cwl/stge26a0514-04a1-4d6d-ba43-0c9674266874/OceanDNA-b35091.fa --refList OceanDNA-b35091/target_genomes_gtdb.txt --output OceanDNA-b35091/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:36:35,918] [INFO] Task succeeded: fastANI
[2023-03-17 05:36:35,925] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:36:35,925] [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_002310835.1	s__Pseudoalteromonas tetraodonis	98.9016	1179	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	conclusive
GCA_018402495.1	s__Pseudoalteromonas sp018402495	92.3883	1005	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238275.3	s__Pseudoalteromonas undina	90.4328	1099	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	90.0016	1069	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_002221505.1	s__Pseudoalteromonas nigrifaciens	81.3505	745	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	81.1674	734	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	81.0729	686	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	81.0201	699	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	80.9164	730	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	80.9123	709	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000238395.3	s__Pseudoalteromonas arctica	80.8989	749	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	80.8748	718	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-17 05:36:35,927] [INFO] GTDB search result was written to OceanDNA-b35091/result_gtdb.tsv
[2023-03-17 05:36:35,932] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:36:35,937] [INFO] DFAST_QC result json was written to OceanDNA-b35091/dqc_result.json
[2023-03-17 05:36:35,937] [INFO] DFAST_QC completed!
[2023-03-17 05:36:35,937] [INFO] Total running time: 0h1m38s