[2023-03-16 18:22:05,830] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:22:05,830] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:22:05,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference
[2023-03-16 18:22:09,499] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:22:09,500] [INFO] Task started: Prodigal
[2023-03-16 18:22:09,500] [INFO] Running command: cat /var/lib/cwl/stgc3014246-a237-474b-be6b-6dc9e0943a68/OceanDNA-b34913.fa | prodigal -d OceanDNA-b34913/cds.fna -a OceanDNA-b34913/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:22:47,362] [INFO] Task succeeded: Prodigal
[2023-03-16 18:22:47,362] [INFO] Task started: HMMsearch
[2023-03-16 18:22:47,363] [INFO] Running command: hmmsearch --tblout OceanDNA-b34913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference/reference_markers.hmm OceanDNA-b34913/protein.faa > /dev/null
[2023-03-16 18:22:47,825] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:22:47,825] [INFO] Found 6/6 markers.
[2023-03-16 18:22:47,859] [INFO] Query marker FASTA was written to OceanDNA-b34913/markers.fasta
[2023-03-16 18:22:47,860] [INFO] Task started: Blastn
[2023-03-16 18:22:47,860] [INFO] Running command: blastn -query OceanDNA-b34913/markers.fasta -db /var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference/reference_markers.fasta -out OceanDNA-b34913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:22:48,538] [INFO] Task succeeded: Blastn
[2023-03-16 18:22:48,540] [INFO] Selected 25 target genomes.
[2023-03-16 18:22:48,541] [INFO] Target genome list was writen to OceanDNA-b34913/target_genomes.txt
[2023-03-16 18:22:48,555] [INFO] Task started: fastANI
[2023-03-16 18:22:48,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3014246-a237-474b-be6b-6dc9e0943a68/OceanDNA-b34913.fa --refList OceanDNA-b34913/target_genomes.txt --output OceanDNA-b34913/fastani_result.tsv --threads 1
[2023-03-16 18:23:05,538] [INFO] Task succeeded: fastANI
[2023-03-16 18:23:05,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:23:05,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:23:05,547] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:23:05,547] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:23:05,547] [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
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	81.5289	888	1624	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	79.8468	669	1624	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.809	185	1624	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.2218	117	1624	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.1016	135	1624	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	76.8396	137	1624	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	76.8273	137	1624	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	76.7922	81	1624	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	76.5831	70	1624	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	76.543	58	1624	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	76.3456	58	1624	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	75.6648	67	1624	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:23:05,548] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34913/tc_result.tsv
[2023-03-16 18:23:05,549] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:23:05,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:23:05,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference/checkm_data
[2023-03-16 18:23:05,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:23:05,602] [INFO] Task started: CheckM
[2023-03-16 18:23:05,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34913/checkm_input OceanDNA-b34913/checkm_result
[2023-03-16 18:24:11,394] [INFO] Task succeeded: CheckM
[2023-03-16 18:24:11,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:24:11,405] [INFO] ===== Completeness check finished =====
[2023-03-16 18:24:11,405] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:24:11,405] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34913/markers.fasta)
[2023-03-16 18:24:11,406] [INFO] Task started: Blastn
[2023-03-16 18:24:11,406] [INFO] Running command: blastn -query OceanDNA-b34913/markers.fasta -db /var/lib/cwl/stg1dd12583-6279-4628-897a-dd5e04a473f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:24:12,444] [INFO] Task succeeded: Blastn
[2023-03-16 18:24:12,447] [INFO] Selected 11 target genomes.
[2023-03-16 18:24:12,447] [INFO] Target genome list was writen to OceanDNA-b34913/target_genomes_gtdb.txt
[2023-03-16 18:24:12,453] [INFO] Task started: fastANI
[2023-03-16 18:24:12,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3014246-a237-474b-be6b-6dc9e0943a68/OceanDNA-b34913.fa --refList OceanDNA-b34913/target_genomes_gtdb.txt --output OceanDNA-b34913/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:24:22,830] [INFO] Task succeeded: fastANI
[2023-03-16 18:24:22,836] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:24:22,836] [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_009796745.1	s__Paraglaciecola sp009796745	95.9991	1452	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011378905.1	s__Paraglaciecola sp011378905	90.1754	1352	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	81.5289	888	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	79.8473	669	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	79.8433	651	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000314955.1	s__Paraglaciecola chathamensis	79.6083	617	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	79.4737	626	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	78.041	157	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314995.1	s__Paraglaciecola arctica	77.8148	186	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:24:22,838] [INFO] GTDB search result was written to OceanDNA-b34913/result_gtdb.tsv
[2023-03-16 18:24:22,840] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:24:22,844] [INFO] DFAST_QC result json was written to OceanDNA-b34913/dqc_result.json
[2023-03-16 18:24:22,844] [INFO] DFAST_QC completed!
[2023-03-16 18:24:22,844] [INFO] Total running time: 0h2m17s