[2023-03-16 01:03:15,358] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:03:15,359] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:03:15,359] [INFO] DQC Reference Directory: /var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference
[2023-03-16 01:03:16,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:03:16,538] [INFO] Task started: Prodigal
[2023-03-16 01:03:16,538] [INFO] Running command: cat /var/lib/cwl/stg238084f6-cc40-4493-88ba-6e236af68768/OceanDNA-b34384.fa | prodigal -d OceanDNA-b34384/cds.fna -a OceanDNA-b34384/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:03:39,612] [INFO] Task succeeded: Prodigal
[2023-03-16 01:03:39,612] [INFO] Task started: HMMsearch
[2023-03-16 01:03:39,612] [INFO] Running command: hmmsearch --tblout OceanDNA-b34384/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference/reference_markers.hmm OceanDNA-b34384/protein.faa > /dev/null
[2023-03-16 01:03:39,851] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:03:39,851] [INFO] Found 6/6 markers.
[2023-03-16 01:03:39,877] [INFO] Query marker FASTA was written to OceanDNA-b34384/markers.fasta
[2023-03-16 01:03:39,878] [INFO] Task started: Blastn
[2023-03-16 01:03:39,878] [INFO] Running command: blastn -query OceanDNA-b34384/markers.fasta -db /var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference/reference_markers.fasta -out OceanDNA-b34384/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:03:40,546] [INFO] Task succeeded: Blastn
[2023-03-16 01:03:40,546] [INFO] Selected 11 target genomes.
[2023-03-16 01:03:40,547] [INFO] Target genome list was writen to OceanDNA-b34384/target_genomes.txt
[2023-03-16 01:03:40,556] [INFO] Task started: fastANI
[2023-03-16 01:03:40,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg238084f6-cc40-4493-88ba-6e236af68768/OceanDNA-b34384.fa --refList OceanDNA-b34384/target_genomes.txt --output OceanDNA-b34384/fastani_result.tsv --threads 1
[2023-03-16 01:03:49,651] [INFO] Task succeeded: fastANI
[2023-03-16 01:03:49,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:03:49,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:03:49,657] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 01:03:49,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 01:03:49,658] [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 gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	97.4728	1242	1383	95	conclusive
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	83.6302	938	1383	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	83.4156	896	1383	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	83.2962	923	1383	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	83.1267	888	1383	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.699	413	1383	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:03:49,658] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34384/tc_result.tsv
[2023-03-16 01:03:49,658] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:03:49,658] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:03:49,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference/checkm_data
[2023-03-16 01:03:49,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:03:49,664] [INFO] Task started: CheckM
[2023-03-16 01:03:49,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34384/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34384/checkm_input OceanDNA-b34384/checkm_result
[2023-03-16 01:04:51,931] [INFO] Task succeeded: CheckM
[2023-03-16 01:04:51,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:04:51,937] [INFO] ===== Completeness check finished =====
[2023-03-16 01:04:51,937] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:04:51,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34384/markers.fasta)
[2023-03-16 01:04:51,939] [INFO] Task started: Blastn
[2023-03-16 01:04:51,939] [INFO] Running command: blastn -query OceanDNA-b34384/markers.fasta -db /var/lib/cwl/stg0581d006-5bf0-49ac-a91a-52c30be83c6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34384/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:04:53,433] [INFO] Task succeeded: Blastn
[2023-03-16 01:04:53,435] [INFO] Selected 12 target genomes.
[2023-03-16 01:04:53,435] [INFO] Target genome list was writen to OceanDNA-b34384/target_genomes_gtdb.txt
[2023-03-16 01:04:54,068] [INFO] Task started: fastANI
[2023-03-16 01:04:54,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg238084f6-cc40-4493-88ba-6e236af68768/OceanDNA-b34384.fa --refList OceanDNA-b34384/target_genomes_gtdb.txt --output OceanDNA-b34384/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:05:06,139] [INFO] Task succeeded: fastANI
[2023-03-16 01:05:06,147] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:05:06,147] [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_002993325.1	s__Alteromonas gracilis	97.4728	1242	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	conclusive
GCF_016405965.1	s__Alteromonas sp016405965	91.2155	1212	1383	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	84.0784	914	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_009811415.1	s__Alteromonas sp009811415	83.7163	1010	1383	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	83.6505	937	1383	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	83.4118	896	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_000020585.3	s__Alteromonas mediterranea	83.2893	925	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_005117025.1	s__Alteromonas portus	83.1226	888	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	83.0176	888	1383	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	82.9997	899	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_003443615.1	s__Alteromonas sp003443615	82.9441	898	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016756315.1	s__Alteromonas sp009811495	80.9858	562	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
--------------------------------------------------------------------------------
[2023-03-16 01:05:06,148] [INFO] GTDB search result was written to OceanDNA-b34384/result_gtdb.tsv
[2023-03-16 01:05:06,149] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:05:06,150] [INFO] DFAST_QC result json was written to OceanDNA-b34384/dqc_result.json
[2023-03-16 01:05:06,150] [INFO] DFAST_QC completed!
[2023-03-16 01:05:06,151] [INFO] Total running time: 0h1m51s