[2023-03-15 12:33:51,665] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,665] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference
[2023-03-15 12:33:52,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,753] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,753] [INFO] Running command: cat /var/lib/cwl/stgb6ae6e26-9e37-46c2-a391-970ced34aa2c/OceanDNA-b17181.fa | prodigal -d OceanDNA-b17181/cds.fna -a OceanDNA-b17181/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:33:59,091] [INFO] Task succeeded: Prodigal
[2023-03-15 12:33:59,091] [INFO] Task started: HMMsearch
[2023-03-15 12:33:59,091] [INFO] Running command: hmmsearch --tblout OceanDNA-b17181/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference/reference_markers.hmm OceanDNA-b17181/protein.faa > /dev/null
[2023-03-15 12:33:59,249] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:33:59,249] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb6ae6e26-9e37-46c2-a391-970ced34aa2c/OceanDNA-b17181.fa]
[2023-03-15 12:33:59,264] [INFO] Query marker FASTA was written to OceanDNA-b17181/markers.fasta
[2023-03-15 12:33:59,265] [INFO] Task started: Blastn
[2023-03-15 12:33:59,266] [INFO] Running command: blastn -query OceanDNA-b17181/markers.fasta -db /var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference/reference_markers.fasta -out OceanDNA-b17181/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:33:59,711] [INFO] Task succeeded: Blastn
[2023-03-15 12:33:59,713] [INFO] Selected 8 target genomes.
[2023-03-15 12:33:59,713] [INFO] Target genome list was writen to OceanDNA-b17181/target_genomes.txt
[2023-03-15 12:33:59,717] [INFO] Task started: fastANI
[2023-03-15 12:33:59,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ae6e26-9e37-46c2-a391-970ced34aa2c/OceanDNA-b17181.fa --refList OceanDNA-b17181/target_genomes.txt --output OceanDNA-b17181/fastani_result.tsv --threads 1
[2023-03-15 12:34:03,552] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:03,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:03,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:03,558] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 12:34:03,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 12:34:03,558] [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
Salinicoccus roseus	strain=CCM 3516	GCA_014634945.1	45670	45670	type	True	97.88	246	251	95	conclusive
Salinicoccus roseus	strain=DSM 5351	GCA_003814515.1	45670	45670	type	True	97.8637	247	251	95	conclusive
Salinicoccus luteus	strain=DSM 17002	GCA_000712035.1	367840	367840	type	True	88.8416	241	251	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	80.2513	176	251	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	79.9821	166	251	95	below_threshold
Salinicoccus sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	78.4396	98	251	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:03,674] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17181/tc_result.tsv
[2023-03-15 12:34:03,677] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:03,677] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:03,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference/checkm_data
[2023-03-15 12:34:03,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:03,683] [INFO] Task started: CheckM
[2023-03-15 12:34:03,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17181/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17181/checkm_input OceanDNA-b17181/checkm_result
[2023-03-15 12:34:26,291] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:26,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.99%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:26,304] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:26,304] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:26,304] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17181/markers.fasta)
[2023-03-15 12:34:26,306] [INFO] Task started: Blastn
[2023-03-15 12:34:26,306] [INFO] Running command: blastn -query OceanDNA-b17181/markers.fasta -db /var/lib/cwl/stg96cbb0fe-5ec7-4fa6-b3d2-07427aae854b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17181/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:26,765] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:26,769] [INFO] Selected 12 target genomes.
[2023-03-15 12:34:26,769] [INFO] Target genome list was writen to OceanDNA-b17181/target_genomes_gtdb.txt
[2023-03-15 12:34:26,819] [INFO] Task started: fastANI
[2023-03-15 12:34:26,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ae6e26-9e37-46c2-a391-970ced34aa2c/OceanDNA-b17181.fa --refList OceanDNA-b17181/target_genomes_gtdb.txt --output OceanDNA-b17181/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:34:32,720] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:32,724] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:34:32,724] [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_003814515.1	s__Salinicoccus roseus	97.8637	247	251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	97.90	96.75	0.92	0.87	5	conclusive
GCF_000712035.1	s__Salinicoccus luteus	88.8416	241	251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713705.1	s__Salinicoccus cyprini	80.2513	176	251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831115.1	s__Salinicoccus hispanicus	79.9821	166	251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000986795.1	s__Salinicoccus sediminis	78.4396	98	251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:34:32,725] [INFO] GTDB search result was written to OceanDNA-b17181/result_gtdb.tsv
[2023-03-15 12:34:32,725] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:34:32,726] [INFO] DFAST_QC result json was written to OceanDNA-b17181/dqc_result.json
[2023-03-15 12:34:32,726] [INFO] DFAST_QC completed!
[2023-03-15 12:34:32,726] [INFO] Total running time: 0h0m41s