[2023-03-16 06:01:02,991] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:01:02,995] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:01:02,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference
[2023-03-16 06:01:04,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:01:04,091] [INFO] Task started: Prodigal
[2023-03-16 06:01:04,092] [INFO] Running command: cat /var/lib/cwl/stg86bea10e-085d-4f81-8f40-292a42edbb93/OceanDNA-b34544.fa | prodigal -d OceanDNA-b34544/cds.fna -a OceanDNA-b34544/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:01:23,933] [INFO] Task succeeded: Prodigal
[2023-03-16 06:01:23,934] [INFO] Task started: HMMsearch
[2023-03-16 06:01:23,934] [INFO] Running command: hmmsearch --tblout OceanDNA-b34544/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference/reference_markers.hmm OceanDNA-b34544/protein.faa > /dev/null
[2023-03-16 06:01:24,164] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:01:24,165] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg86bea10e-085d-4f81-8f40-292a42edbb93/OceanDNA-b34544.fa]
[2023-03-16 06:01:24,225] [INFO] Query marker FASTA was written to OceanDNA-b34544/markers.fasta
[2023-03-16 06:01:24,227] [INFO] Task started: Blastn
[2023-03-16 06:01:24,227] [INFO] Running command: blastn -query OceanDNA-b34544/markers.fasta -db /var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference/reference_markers.fasta -out OceanDNA-b34544/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:01:24,855] [INFO] Task succeeded: Blastn
[2023-03-16 06:01:24,868] [INFO] Selected 12 target genomes.
[2023-03-16 06:01:24,869] [INFO] Target genome list was writen to OceanDNA-b34544/target_genomes.txt
[2023-03-16 06:01:24,876] [INFO] Task started: fastANI
[2023-03-16 06:01:24,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg86bea10e-085d-4f81-8f40-292a42edbb93/OceanDNA-b34544.fa --refList OceanDNA-b34544/target_genomes.txt --output OceanDNA-b34544/fastani_result.tsv --threads 1
[2023-03-16 06:01:34,235] [INFO] Task succeeded: fastANI
[2023-03-16 06:01:34,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:01:34,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:01:34,242] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 06:01:34,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 06:01:34,242] [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 mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	99.3541	1138	1191	95	conclusive
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	82.7542	818	1191	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	82.6351	782	1191	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	82.5171	789	1191	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	82.3991	769	1191	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	79.9862	347	1191	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	79.11	341	1191	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:01:34,248] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34544/tc_result.tsv
[2023-03-16 06:01:34,254] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:01:34,254] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:01:34,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference/checkm_data
[2023-03-16 06:01:34,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:01:34,437] [INFO] Task started: CheckM
[2023-03-16 06:01:34,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34544/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34544/checkm_input OceanDNA-b34544/checkm_result
[2023-03-16 06:02:24,776] [INFO] Task succeeded: CheckM
[2023-03-16 06:02:24,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:02:24,784] [INFO] ===== Completeness check finished =====
[2023-03-16 06:02:24,784] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:02:24,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34544/markers.fasta)
[2023-03-16 06:02:24,786] [INFO] Task started: Blastn
[2023-03-16 06:02:24,786] [INFO] Running command: blastn -query OceanDNA-b34544/markers.fasta -db /var/lib/cwl/stg9d374809-8756-4d7b-a8ef-ec83619b4567/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34544/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:02:25,850] [INFO] Task succeeded: Blastn
[2023-03-16 06:02:25,853] [INFO] Selected 10 target genomes.
[2023-03-16 06:02:25,853] [INFO] Target genome list was writen to OceanDNA-b34544/target_genomes_gtdb.txt
[2023-03-16 06:02:25,859] [INFO] Task started: fastANI
[2023-03-16 06:02:25,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg86bea10e-085d-4f81-8f40-292a42edbb93/OceanDNA-b34544.fa --refList OceanDNA-b34544/target_genomes_gtdb.txt --output OceanDNA-b34544/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:02:34,968] [INFO] Task succeeded: fastANI
[2023-03-16 06:02:34,975] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:02:34,975] [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_000020585.3	s__Alteromonas mediterranea	99.3541	1138	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	conclusive
GCF_016405965.1	s__Alteromonas sp016405965	84.0077	807	1191	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	82.9797	814	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_903772925.1	s__Alteromonas macleodii_A	82.8659	849	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	82.8465	778	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000172635.2	s__Alteromonas macleodii	82.7442	819	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_005117025.1	s__Alteromonas portus	82.635	782	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000597705.1	s__Alteromonas sp000597705	82.6217	831	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_001953635.1	s__Alteromonas abrolhosensis	82.5346	787	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_002993325.1	s__Alteromonas gracilis	82.4044	768	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-16 06:02:34,978] [INFO] GTDB search result was written to OceanDNA-b34544/result_gtdb.tsv
[2023-03-16 06:02:34,982] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:02:34,987] [INFO] DFAST_QC result json was written to OceanDNA-b34544/dqc_result.json
[2023-03-16 06:02:34,987] [INFO] DFAST_QC completed!
[2023-03-16 06:02:34,987] [INFO] Total running time: 0h1m32s