[2023-03-18 23:11:06,916] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,916] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference
[2023-03-18 23:11:08,262] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,262] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,262] [INFO] Running command: cat /var/lib/cwl/stgf33e21df-94ee-48fc-8b52-3a87fffdc290/OceanDNA-b29482.fa | prodigal -d OceanDNA-b29482/cds.fna -a OceanDNA-b29482/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:31,812] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:31,812] [INFO] Task started: HMMsearch
[2023-03-18 23:11:31,812] [INFO] Running command: hmmsearch --tblout OceanDNA-b29482/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference/reference_markers.hmm OceanDNA-b29482/protein.faa > /dev/null
[2023-03-18 23:11:32,087] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:32,088] [INFO] Found 6/6 markers.
[2023-03-18 23:11:32,113] [INFO] Query marker FASTA was written to OceanDNA-b29482/markers.fasta
[2023-03-18 23:11:32,113] [INFO] Task started: Blastn
[2023-03-18 23:11:32,113] [INFO] Running command: blastn -query OceanDNA-b29482/markers.fasta -db /var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference/reference_markers.fasta -out OceanDNA-b29482/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:33,107] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:33,108] [INFO] Selected 12 target genomes.
[2023-03-18 23:11:33,108] [INFO] Target genome list was writen to OceanDNA-b29482/target_genomes.txt
[2023-03-18 23:11:33,116] [INFO] Task started: fastANI
[2023-03-18 23:11:33,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgf33e21df-94ee-48fc-8b52-3a87fffdc290/OceanDNA-b29482.fa --refList OceanDNA-b29482/target_genomes.txt --output OceanDNA-b29482/fastani_result.tsv --threads 1
[2023-03-18 23:11:42,885] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:42,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:42,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:42,893] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:11:42,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:11:42,893] [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
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	98.2094	1026	1231	95	conclusive
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	87.2362	803	1231	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	87.1783	875	1231	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	87.1551	886	1231	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	87.1404	813	1231	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	86.4339	822	1231	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	85.2682	828	1231	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4153	384	1231	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3771	392	1231	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.2967	413	1231	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9076	373	1231	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8302	344	1231	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:11:42,894] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29482/tc_result.tsv
[2023-03-18 23:11:42,894] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:42,894] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:42,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference/checkm_data
[2023-03-18 23:11:42,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:42,900] [INFO] Task started: CheckM
[2023-03-18 23:11:42,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29482/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29482/checkm_input OceanDNA-b29482/checkm_result
[2023-03-18 23:12:43,195] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:43,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:43,198] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:43,199] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:43,199] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29482/markers.fasta)
[2023-03-18 23:12:43,199] [INFO] Task started: Blastn
[2023-03-18 23:12:43,199] [INFO] Running command: blastn -query OceanDNA-b29482/markers.fasta -db /var/lib/cwl/stg97ff9ad0-043d-4f5e-884c-88faa056bef6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29482/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:45,185] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:45,185] [INFO] Selected 6 target genomes.
[2023-03-18 23:12:45,185] [INFO] Target genome list was writen to OceanDNA-b29482/target_genomes_gtdb.txt
[2023-03-18 23:12:45,198] [INFO] Task started: fastANI
[2023-03-18 23:12:45,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgf33e21df-94ee-48fc-8b52-3a87fffdc290/OceanDNA-b29482.fa --refList OceanDNA-b29482/target_genomes_gtdb.txt --output OceanDNA-b29482/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:50,764] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:50,769] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:50,769] [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_000466965.1	s__Limimaricola cinnabarinus	98.2094	1026	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002723615.1	s__Limimaricola cinnabarinus_B	88.0712	871	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	87.2203	804	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900172345.1	s__Limimaricola soesokkakensis	87.1901	874	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014195545.1	s__Limimaricola variabilis	86.424	822	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	85.2961	826	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:50,769] [INFO] GTDB search result was written to OceanDNA-b29482/result_gtdb.tsv
[2023-03-18 23:12:50,769] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:50,770] [INFO] DFAST_QC result json was written to OceanDNA-b29482/dqc_result.json
[2023-03-18 23:12:50,770] [INFO] DFAST_QC completed!
[2023-03-18 23:12:50,770] [INFO] Total running time: 0h1m44s