[2023-03-17 04:15:15,031] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:15,031] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:15,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference
[2023-03-17 04:15:16,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,760] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,760] [INFO] Running command: cat /var/lib/cwl/stg2c51471a-cd2d-4494-b6e5-7c8678cd7fbf/OceanDNA-b34303.fa | prodigal -d OceanDNA-b34303/cds.fna -a OceanDNA-b34303/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:33,564] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:33,565] [INFO] Task started: HMMsearch
[2023-03-17 04:15:33,565] [INFO] Running command: hmmsearch --tblout OceanDNA-b34303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference/reference_markers.hmm OceanDNA-b34303/protein.faa > /dev/null
[2023-03-17 04:15:33,777] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:33,777] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2c51471a-cd2d-4494-b6e5-7c8678cd7fbf/OceanDNA-b34303.fa]
[2023-03-17 04:15:33,797] [INFO] Query marker FASTA was written to OceanDNA-b34303/markers.fasta
[2023-03-17 04:15:33,798] [INFO] Task started: Blastn
[2023-03-17 04:15:33,798] [INFO] Running command: blastn -query OceanDNA-b34303/markers.fasta -db /var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference/reference_markers.fasta -out OceanDNA-b34303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:34,367] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:34,368] [INFO] Selected 15 target genomes.
[2023-03-17 04:15:34,368] [INFO] Target genome list was writen to OceanDNA-b34303/target_genomes.txt
[2023-03-17 04:15:34,376] [INFO] Task started: fastANI
[2023-03-17 04:15:34,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c51471a-cd2d-4494-b6e5-7c8678cd7fbf/OceanDNA-b34303.fa --refList OceanDNA-b34303/target_genomes.txt --output OceanDNA-b34303/fastani_result.tsv --threads 1
[2023-03-17 04:15:45,878] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:45,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:45,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:45,884] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:45,885] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:45,885] [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
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	86.0339	814	1033	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	85.4878	786	1033	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	84.613	729	1033	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	83.7427	707	1033	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	82.5535	694	1033	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.1477	278	1033	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.6789	288	1033	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	78.3857	265	1033	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:45,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34303/tc_result.tsv
[2023-03-17 04:15:45,885] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:45,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:45,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference/checkm_data
[2023-03-17 04:15:45,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:45,891] [INFO] Task started: CheckM
[2023-03-17 04:15:45,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34303/checkm_input OceanDNA-b34303/checkm_result
[2023-03-17 04:16:29,559] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:29,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.63%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:29,562] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:29,562] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:29,563] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34303/markers.fasta)
[2023-03-17 04:16:29,563] [INFO] Task started: Blastn
[2023-03-17 04:16:29,563] [INFO] Running command: blastn -query OceanDNA-b34303/markers.fasta -db /var/lib/cwl/stg02c1d459-a757-4848-8016-9040b7442ec0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:30,343] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:30,344] [INFO] Selected 10 target genomes.
[2023-03-17 04:16:30,344] [INFO] Target genome list was writen to OceanDNA-b34303/target_genomes_gtdb.txt
[2023-03-17 04:16:30,351] [INFO] Task started: fastANI
[2023-03-17 04:16:30,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c51471a-cd2d-4494-b6e5-7c8678cd7fbf/OceanDNA-b34303.fa --refList OceanDNA-b34303/target_genomes_gtdb.txt --output OceanDNA-b34303/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:39,164] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:39,170] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:39,171] [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_903772925.1	s__Alteromonas macleodii_A	89.7356	891	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443615.1	s__Alteromonas sp003443615	88.1881	876	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000808575.1	s__Alteromonas marina	86.7318	832	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000597705.1	s__Alteromonas sp000597705	86.215	834	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_005117025.1	s__Alteromonas portus	86.0339	814	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	85.5019	785	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_001953635.1	s__Alteromonas abrolhosensis	84.613	729	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_001885075.1	s__Alteromonas sp001885075	83.96	595	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020585.3	s__Alteromonas mediterranea	83.7427	707	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_016405965.1	s__Alteromonas sp016405965	82.6627	661	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:39,171] [INFO] GTDB search result was written to OceanDNA-b34303/result_gtdb.tsv
[2023-03-17 04:16:39,171] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:39,172] [INFO] DFAST_QC result json was written to OceanDNA-b34303/dqc_result.json
[2023-03-17 04:16:39,172] [INFO] DFAST_QC completed!
[2023-03-17 04:16:39,172] [INFO] Total running time: 0h1m24s