[2023-03-19 01:12:13,946] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:13,946] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:13,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference
[2023-03-19 01:12:15,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:15,733] [INFO] Task started: Prodigal
[2023-03-19 01:12:15,733] [INFO] Running command: cat /var/lib/cwl/stg3fbb500b-d8ec-42fb-8f78-6f7c8c174454/OceanDNA-b35155.fa | prodigal -d OceanDNA-b35155/cds.fna -a OceanDNA-b35155/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:36,806] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:36,807] [INFO] Task started: HMMsearch
[2023-03-19 01:12:36,807] [INFO] Running command: hmmsearch --tblout OceanDNA-b35155/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference/reference_markers.hmm OceanDNA-b35155/protein.faa > /dev/null
[2023-03-19 01:12:37,002] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:37,003] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3fbb500b-d8ec-42fb-8f78-6f7c8c174454/OceanDNA-b35155.fa]
[2023-03-19 01:12:37,024] [INFO] Query marker FASTA was written to OceanDNA-b35155/markers.fasta
[2023-03-19 01:12:37,025] [INFO] Task started: Blastn
[2023-03-19 01:12:37,025] [INFO] Running command: blastn -query OceanDNA-b35155/markers.fasta -db /var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference/reference_markers.fasta -out OceanDNA-b35155/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:37,728] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:37,729] [INFO] Selected 13 target genomes.
[2023-03-19 01:12:37,729] [INFO] Target genome list was writen to OceanDNA-b35155/target_genomes.txt
[2023-03-19 01:12:37,738] [INFO] Task started: fastANI
[2023-03-19 01:12:37,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fbb500b-d8ec-42fb-8f78-6f7c8c174454/OceanDNA-b35155.fa --refList OceanDNA-b35155/target_genomes.txt --output OceanDNA-b35155/fastani_result.tsv --threads 1
[2023-03-19 01:12:50,326] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:50,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:50,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:50,335] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:50,335] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:12:50,335] [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
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	93.9695	1004	1102	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	85.5835	918	1102	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	85.4765	916	1102	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	85.1213	849	1102	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	85.0978	870	1102	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	84.4556	868	1102	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	84.2984	789	1102	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	83.6632	839	1102	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.4237	710	1102	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.9678	578	1102	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.9495	567	1102	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.7035	390	1102	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.4193	391	1102	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:12:50,336] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35155/tc_result.tsv
[2023-03-19 01:12:50,336] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:50,336] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:50,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference/checkm_data
[2023-03-19 01:12:50,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:50,342] [INFO] Task started: CheckM
[2023-03-19 01:12:50,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35155/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35155/checkm_input OceanDNA-b35155/checkm_result
[2023-03-19 01:13:41,791] [INFO] Task succeeded: CheckM
[2023-03-19 01:13:41,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:13:41,794] [INFO] ===== Completeness check finished =====
[2023-03-19 01:13:41,794] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:13:41,794] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35155/markers.fasta)
[2023-03-19 01:13:41,795] [INFO] Task started: Blastn
[2023-03-19 01:13:41,795] [INFO] Running command: blastn -query OceanDNA-b35155/markers.fasta -db /var/lib/cwl/stg356a9f63-95e5-42ad-bbc8-d2346e983c41/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35155/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:42,867] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:42,868] [INFO] Selected 5 target genomes.
[2023-03-19 01:13:42,868] [INFO] Target genome list was writen to OceanDNA-b35155/target_genomes_gtdb.txt
[2023-03-19 01:13:42,874] [INFO] Task started: fastANI
[2023-03-19 01:13:42,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fbb500b-d8ec-42fb-8f78-6f7c8c174454/OceanDNA-b35155.fa --refList OceanDNA-b35155/target_genomes_gtdb.txt --output OceanDNA-b35155/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:13:48,549] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:48,553] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:13:48,553] [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_900068835.1	s__Pantoea ludwigii_B	95.7115	1016	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	conclusive
GCF_002858935.1	s__Pantoea endophytica	93.9695	1004	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_900068845.1	s__Pantoea ludwigii_A	91.2016	971	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187905.1	s__Pantoea sp001187905	90.0054	966	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCA_900215435.1	s__Pantoea sp900215435	88.7843	913	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.51	99.02	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-19 01:13:48,554] [INFO] GTDB search result was written to OceanDNA-b35155/result_gtdb.tsv
[2023-03-19 01:13:48,554] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:13:48,555] [INFO] DFAST_QC result json was written to OceanDNA-b35155/dqc_result.json
[2023-03-19 01:13:48,555] [INFO] DFAST_QC completed!
[2023-03-19 01:13:48,555] [INFO] Total running time: 0h1m35s