[2023-03-18 00:35:04,590] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,590] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference
[2023-03-18 00:35:05,692] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,692] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,692] [INFO] Running command: cat /var/lib/cwl/stge39a604d-ce15-4be7-8ec4-7207fd3b040d/OceanDNA-b35020.fa | prodigal -d OceanDNA-b35020/cds.fna -a OceanDNA-b35020/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:24,142] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:24,142] [INFO] Task started: HMMsearch
[2023-03-18 00:35:24,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b35020/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference/reference_markers.hmm OceanDNA-b35020/protein.faa > /dev/null
[2023-03-18 00:35:24,532] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:24,532] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge39a604d-ce15-4be7-8ec4-7207fd3b040d/OceanDNA-b35020.fa]
[2023-03-18 00:35:24,555] [INFO] Query marker FASTA was written to OceanDNA-b35020/markers.fasta
[2023-03-18 00:35:24,556] [INFO] Task started: Blastn
[2023-03-18 00:35:24,556] [INFO] Running command: blastn -query OceanDNA-b35020/markers.fasta -db /var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference/reference_markers.fasta -out OceanDNA-b35020/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:25,144] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:25,145] [INFO] Selected 12 target genomes.
[2023-03-18 00:35:25,145] [INFO] Target genome list was writen to OceanDNA-b35020/target_genomes.txt
[2023-03-18 00:35:25,151] [INFO] Task started: fastANI
[2023-03-18 00:35:25,151] [INFO] Running command: fastANI --query /var/lib/cwl/stge39a604d-ce15-4be7-8ec4-7207fd3b040d/OceanDNA-b35020.fa --refList OceanDNA-b35020/target_genomes.txt --output OceanDNA-b35020/fastani_result.tsv --threads 1
[2023-03-18 00:35:36,051] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:36,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:36,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:36,058] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:36,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:35:36,058] [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 shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	93.858	1034	1150	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	92.5769	1041	1150	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	92.4867	1030	1150	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	85.9739	851	1150	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	83.131	841	1150	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	83.1081	829	1150	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	79.2423	505	1150	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	78.9394	487	1150	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.8761	435	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:35:36,059] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35020/tc_result.tsv
[2023-03-18 00:35:36,059] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:36,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:36,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference/checkm_data
[2023-03-18 00:35:36,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:36,066] [INFO] Task started: CheckM
[2023-03-18 00:35:36,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35020/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35020/checkm_input OceanDNA-b35020/checkm_result
[2023-03-18 00:36:23,414] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:23,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:23,418] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:23,418] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:23,418] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35020/markers.fasta)
[2023-03-18 00:36:23,418] [INFO] Task started: Blastn
[2023-03-18 00:36:23,418] [INFO] Running command: blastn -query OceanDNA-b35020/markers.fasta -db /var/lib/cwl/stg0ae26183-8b56-4c1c-871c-922d1058a5c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35020/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:24,220] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:24,221] [INFO] Selected 7 target genomes.
[2023-03-18 00:36:24,221] [INFO] Target genome list was writen to OceanDNA-b35020/target_genomes_gtdb.txt
[2023-03-18 00:36:24,229] [INFO] Task started: fastANI
[2023-03-18 00:36:24,232] [INFO] Running command: fastANI --query /var/lib/cwl/stge39a604d-ce15-4be7-8ec4-7207fd3b040d/OceanDNA-b35020.fa --refList OceanDNA-b35020/target_genomes_gtdb.txt --output OceanDNA-b35020/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:30,769] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:30,774] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:36:30,774] [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_001306915.1	s__Pseudoalteromonas lipolytica_A	98.3073	1121	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	conclusive
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	93.8665	1033	1150	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	93.737	992	1150	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	93.7172	1018	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCA_002684115.1	s__Pseudoalteromonas sp002684115	93.6559	192	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	97.90	97.71	0.79	0.79	5	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	93.5628	1027	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	92.5769	1041	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:30,774] [INFO] GTDB search result was written to OceanDNA-b35020/result_gtdb.tsv
[2023-03-18 00:36:30,774] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:30,775] [INFO] DFAST_QC result json was written to OceanDNA-b35020/dqc_result.json
[2023-03-18 00:36:30,775] [INFO] DFAST_QC completed!
[2023-03-18 00:36:30,775] [INFO] Total running time: 0h1m26s