[2023-03-19 00:44:19,966] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,966] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference
[2023-03-19 00:44:21,064] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,064] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,064] [INFO] Running command: cat /var/lib/cwl/stg66ec20ae-fe9e-4f5e-9587-9d0d27bacb04/OceanDNA-b30570.fa | prodigal -d OceanDNA-b30570/cds.fna -a OceanDNA-b30570/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:43,016] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:43,016] [INFO] Task started: HMMsearch
[2023-03-19 00:44:43,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b30570/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference/reference_markers.hmm OceanDNA-b30570/protein.faa > /dev/null
[2023-03-19 00:44:43,221] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:43,222] [INFO] Found 6/6 markers.
[2023-03-19 00:44:43,245] [INFO] Query marker FASTA was written to OceanDNA-b30570/markers.fasta
[2023-03-19 00:44:43,246] [INFO] Task started: Blastn
[2023-03-19 00:44:43,246] [INFO] Running command: blastn -query OceanDNA-b30570/markers.fasta -db /var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference/reference_markers.fasta -out OceanDNA-b30570/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:44,075] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:44,076] [INFO] Selected 8 target genomes.
[2023-03-19 00:44:44,076] [INFO] Target genome list was writen to OceanDNA-b30570/target_genomes.txt
[2023-03-19 00:44:44,082] [INFO] Task started: fastANI
[2023-03-19 00:44:44,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ec20ae-fe9e-4f5e-9587-9d0d27bacb04/OceanDNA-b30570.fa --refList OceanDNA-b30570/target_genomes.txt --output OceanDNA-b30570/fastani_result.tsv --threads 1
[2023-03-19 00:44:51,317] [INFO] Task succeeded: fastANI
[2023-03-19 00:44:51,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:44:51,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:44:51,323] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 00:44:51,324] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-19 00:44:51,324] [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
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	96.4834	1158	1202	95	inconclusive
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	96.2309	1148	1202	95	inconclusive
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	91.5569	1029	1202	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	85.3346	835	1202	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	85.0685	839	1202	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	84.3012	837	1202	95	below_threshold
Thioclava dalianensis	strain=DLFJ1-1	GCA_000715505.1	1185766	1185766	type	True	81.1222	697	1202	95	below_threshold
Thioclava dalianensis	strain=CGMCC 1.12325	GCA_900115035.1	1185766	1185766	type	True	81.0654	719	1202	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:44:51,324] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30570/tc_result.tsv
[2023-03-19 00:44:51,324] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:44:51,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:44:51,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference/checkm_data
[2023-03-19 00:44:51,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:44:51,347] [INFO] Task started: CheckM
[2023-03-19 00:44:51,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30570/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30570/checkm_input OceanDNA-b30570/checkm_result
[2023-03-19 00:45:45,571] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:45,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:45,574] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:45,574] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:45,575] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30570/markers.fasta)
[2023-03-19 00:45:45,576] [INFO] Task started: Blastn
[2023-03-19 00:45:45,576] [INFO] Running command: blastn -query OceanDNA-b30570/markers.fasta -db /var/lib/cwl/stgca451411-4964-437d-930e-1b035a252faa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30570/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:47,055] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:47,056] [INFO] Selected 5 target genomes.
[2023-03-19 00:45:47,056] [INFO] Target genome list was writen to OceanDNA-b30570/target_genomes_gtdb.txt
[2023-03-19 00:45:47,061] [INFO] Task started: fastANI
[2023-03-19 00:45:47,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ec20ae-fe9e-4f5e-9587-9d0d27bacb04/OceanDNA-b30570.fa --refList OceanDNA-b30570/target_genomes_gtdb.txt --output OceanDNA-b30570/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:45:52,033] [INFO] Task succeeded: fastANI
[2023-03-19 00:45:52,037] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:45:52,037] [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_002020355.1	s__Thioclava sediminum	96.4834	1158	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	conclusive
GCF_002085925.2	s__Thioclava electrotropha	96.2309	1148	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	-
GCF_009296265.1	s__Thioclava sp009296265	96.1788	1143	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	94.9733	1072	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_001940525.2	s__Thioclava nitratireducens	91.5569	1029	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
--------------------------------------------------------------------------------
[2023-03-19 00:45:52,038] [INFO] GTDB search result was written to OceanDNA-b30570/result_gtdb.tsv
[2023-03-19 00:45:52,038] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:45:52,040] [INFO] DFAST_QC result json was written to OceanDNA-b30570/dqc_result.json
[2023-03-19 00:45:52,040] [INFO] DFAST_QC completed!
[2023-03-19 00:45:52,040] [INFO] Total running time: 0h1m32s