[2023-03-18 04:54:25,331] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:54:25,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:54:25,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference
[2023-03-18 04:54:26,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:54:26,989] [INFO] Task started: Prodigal
[2023-03-18 04:54:26,989] [INFO] Running command: cat /var/lib/cwl/stge4f1a3f8-3f42-401b-931d-a05f76bed01e/OceanDNA-b34266.fa | prodigal -d OceanDNA-b34266/cds.fna -a OceanDNA-b34266/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:54:53,046] [INFO] Task succeeded: Prodigal
[2023-03-18 04:54:53,046] [INFO] Task started: HMMsearch
[2023-03-18 04:54:53,046] [INFO] Running command: hmmsearch --tblout OceanDNA-b34266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference/reference_markers.hmm OceanDNA-b34266/protein.faa > /dev/null
[2023-03-18 04:54:53,260] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:54:53,260] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge4f1a3f8-3f42-401b-931d-a05f76bed01e/OceanDNA-b34266.fa]
[2023-03-18 04:54:53,286] [INFO] Query marker FASTA was written to OceanDNA-b34266/markers.fasta
[2023-03-18 04:54:53,287] [INFO] Task started: Blastn
[2023-03-18 04:54:53,287] [INFO] Running command: blastn -query OceanDNA-b34266/markers.fasta -db /var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference/reference_markers.fasta -out OceanDNA-b34266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:54:54,043] [INFO] Task succeeded: Blastn
[2023-03-18 04:54:54,044] [INFO] Selected 11 target genomes.
[2023-03-18 04:54:54,044] [INFO] Target genome list was writen to OceanDNA-b34266/target_genomes.txt
[2023-03-18 04:54:54,055] [INFO] Task started: fastANI
[2023-03-18 04:54:54,055] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f1a3f8-3f42-401b-931d-a05f76bed01e/OceanDNA-b34266.fa --refList OceanDNA-b34266/target_genomes.txt --output OceanDNA-b34266/fastani_result.tsv --threads 1
[2023-03-18 04:55:02,962] [INFO] Task succeeded: fastANI
[2023-03-18 04:55:02,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:55:02,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:55:02,970] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2023-03-18 04:55:02,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:55:02,971] [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
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	97.602	1188	1385	95	conclusive
Aeromonas salmonicida subsp. salmonicida	strain=CIP 103209	GCA_000820065.1	29491	645	type	True	97.5718	1260	1385	95	conclusive
Aeromonas salmonicida subsp. salmonicida	strain=ATCC 33658	GCA_001643305.1	29491	645	type	True	97.5495	1261	1385	95	conclusive
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	97.5072	1282	1385	95	conclusive
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_000447435.2	96473	645	type	True	97.2071	1212	1385	95	conclusive
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_002735225.1	96473	645	type	True	97.1632	1261	1385	95	conclusive
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	76.7225	76	1385	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.919	112	1385	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.6595	97	1385	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.656	98	1385	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	75.6535	98	1385	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:55:02,971] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34266/tc_result.tsv
[2023-03-18 04:55:02,971] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:55:02,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:55:02,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference/checkm_data
[2023-03-18 04:55:02,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:55:03,016] [INFO] Task started: CheckM
[2023-03-18 04:55:03,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34266/checkm_input OceanDNA-b34266/checkm_result
[2023-03-18 04:56:07,518] [INFO] Task succeeded: CheckM
[2023-03-18 04:56:07,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:56:07,575] [INFO] ===== Completeness check finished =====
[2023-03-18 04:56:07,575] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:56:07,575] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34266/markers.fasta)
[2023-03-18 04:56:07,577] [INFO] Task started: Blastn
[2023-03-18 04:56:07,577] [INFO] Running command: blastn -query OceanDNA-b34266/markers.fasta -db /var/lib/cwl/stg903dfe94-894a-43c6-a1aa-9fed75b00b8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:56:08,775] [INFO] Task succeeded: Blastn
[2023-03-18 04:56:08,777] [INFO] Selected 9 target genomes.
[2023-03-18 04:56:08,778] [INFO] Target genome list was writen to OceanDNA-b34266/target_genomes_gtdb.txt
[2023-03-18 04:56:08,788] [INFO] Task started: fastANI
[2023-03-18 04:56:08,788] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f1a3f8-3f42-401b-931d-a05f76bed01e/OceanDNA-b34266.fa --refList OceanDNA-b34266/target_genomes_gtdb.txt --output OceanDNA-b34266/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:56:18,519] [INFO] Task succeeded: fastANI
[2023-03-18 04:56:18,525] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:56:18,525] [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_001643305.1	s__Aeromonas salmonicida	97.5495	1261	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	conclusive
GCF_000820005.1	s__Aeromonas piscicola	91.8751	1242	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	-
GCF_000819745.1	s__Aeromonas bestiarum	91.3536	1207	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820025.1	s__Aeromonas popoffii	89.8778	1122	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.17	98.00	0.92	0.89	4	-
GCF_900637545.1	s__Aeromonas encheleia	87.0336	1128	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_000764655.1	s__Aeromonas aquatica	86.4502	1050	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820145.1	s__Aeromonas sobria	85.8757	1046	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.57	95.21	0.89	0.85	13	-
GCF_014204135.1	s__Aeromonas fluvialis_A	85.869	969	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000388115.1	s__Aeromonas molluscorum	83.7594	849	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:56:18,526] [INFO] GTDB search result was written to OceanDNA-b34266/result_gtdb.tsv
[2023-03-18 04:56:18,526] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:56:18,527] [INFO] DFAST_QC result json was written to OceanDNA-b34266/dqc_result.json
[2023-03-18 04:56:18,527] [INFO] DFAST_QC completed!
[2023-03-18 04:56:18,527] [INFO] Total running time: 0h1m53s