[2023-03-14 11:33:34,957] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,957] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference
[2023-03-14 11:33:36,153] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,153] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,153] [INFO] Running command: cat /var/lib/cwl/stg782db4ba-b1e2-46da-a69c-a3860fc1daee/OceanDNA-b34551.fa | prodigal -d OceanDNA-b34551/cds.fna -a OceanDNA-b34551/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:34:01,562] [INFO] Task succeeded: Prodigal
[2023-03-14 11:34:01,562] [INFO] Task started: HMMsearch
[2023-03-14 11:34:01,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b34551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference/reference_markers.hmm OceanDNA-b34551/protein.faa > /dev/null
[2023-03-14 11:34:01,964] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:34:01,965] [INFO] Found 6/6 markers.
[2023-03-14 11:34:01,992] [INFO] Query marker FASTA was written to OceanDNA-b34551/markers.fasta
[2023-03-14 11:34:01,992] [INFO] Task started: Blastn
[2023-03-14 11:34:01,992] [INFO] Running command: blastn -query OceanDNA-b34551/markers.fasta -db /var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference/reference_markers.fasta -out OceanDNA-b34551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:02,692] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:02,693] [INFO] Selected 17 target genomes.
[2023-03-14 11:34:02,693] [INFO] Target genome list was writen to OceanDNA-b34551/target_genomes.txt
[2023-03-14 11:34:02,703] [INFO] Task started: fastANI
[2023-03-14 11:34:02,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg782db4ba-b1e2-46da-a69c-a3860fc1daee/OceanDNA-b34551.fa --refList OceanDNA-b34551/target_genomes.txt --output OceanDNA-b34551/fastani_result.tsv --threads 1
[2023-03-14 11:34:16,594] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:16,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:16,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:16,601] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 11:34:16,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 11:34:16,602] [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 naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	97.8099	1368	1510	95	conclusive
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	93.0465	1269	1510	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	79.7272	456	1510	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	79.3638	434	1510	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	79.3486	422	1510	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	79.1642	401	1510	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	79.1015	412	1510	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.0966	371	1510	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.9987	354	1510	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.8973	404	1510	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	76.5732	50	1510	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:16,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34551/tc_result.tsv
[2023-03-14 11:34:16,602] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:16,602] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:16,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference/checkm_data
[2023-03-14 11:34:16,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:16,609] [INFO] Task started: CheckM
[2023-03-14 11:34:16,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34551/checkm_input OceanDNA-b34551/checkm_result
[2023-03-14 11:35:19,252] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:19,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 5.30%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:19,255] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:19,255] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:19,256] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34551/markers.fasta)
[2023-03-14 11:35:19,256] [INFO] Task started: Blastn
[2023-03-14 11:35:19,256] [INFO] Running command: blastn -query OceanDNA-b34551/markers.fasta -db /var/lib/cwl/stg0c96f84b-93ff-4401-9759-596963db033b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:20,048] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:20,048] [INFO] Selected 11 target genomes.
[2023-03-14 11:35:20,049] [INFO] Target genome list was writen to OceanDNA-b34551/target_genomes_gtdb.txt
[2023-03-14 11:35:20,058] [INFO] Task started: fastANI
[2023-03-14 11:35:20,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg782db4ba-b1e2-46da-a69c-a3860fc1daee/OceanDNA-b34551.fa --refList OceanDNA-b34551/target_genomes_gtdb.txt --output OceanDNA-b34551/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:29,539] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:29,545] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:35:29,545] [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_000213655.1	s__Alteromonas naphthalenivorans	97.8221	1367	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	conclusive
GCF_902506055.1	s__Alteromonas lipotrueae	93.0754	1281	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCA_001562115.1	s__Alteromonas stellipolaris	90.8302	1286	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_018100795.1	s__Alteromonas sp018100795	90.3568	1256	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730385.1	s__Alteromonas australica	79.7445	454	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_016405965.1	s__Alteromonas sp016405965	79.3879	403	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	79.1575	403	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_006538325.1	s__Alteromonas sp006538325	79.0269	351	1510	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	79.0114	423	1510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:29,545] [INFO] GTDB search result was written to OceanDNA-b34551/result_gtdb.tsv
[2023-03-14 11:35:29,545] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:29,546] [INFO] DFAST_QC result json was written to OceanDNA-b34551/dqc_result.json
[2023-03-14 11:35:29,546] [INFO] DFAST_QC completed!
[2023-03-14 11:35:29,546] [INFO] Total running time: 0h1m55s