[2023-03-19 00:29:45,968] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:29:45,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:29:45,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference
[2023-03-19 00:29:47,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:29:47,085] [INFO] Task started: Prodigal
[2023-03-19 00:29:47,085] [INFO] Running command: cat /var/lib/cwl/stg3d218bfc-9829-41a9-88fc-267dd7648c12/OceanDNA-b22890.fa | prodigal -d OceanDNA-b22890/cds.fna -a OceanDNA-b22890/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:30:19,379] [INFO] Task succeeded: Prodigal
[2023-03-19 00:30:19,380] [INFO] Task started: HMMsearch
[2023-03-19 00:30:19,380] [INFO] Running command: hmmsearch --tblout OceanDNA-b22890/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference/reference_markers.hmm OceanDNA-b22890/protein.faa > /dev/null
[2023-03-19 00:30:19,626] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:30:19,626] [INFO] Found 6/6 markers.
[2023-03-19 00:30:19,656] [INFO] Query marker FASTA was written to OceanDNA-b22890/markers.fasta
[2023-03-19 00:30:19,657] [INFO] Task started: Blastn
[2023-03-19 00:30:19,657] [INFO] Running command: blastn -query OceanDNA-b22890/markers.fasta -db /var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference/reference_markers.fasta -out OceanDNA-b22890/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:20,176] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:20,176] [INFO] Selected 13 target genomes.
[2023-03-19 00:30:20,177] [INFO] Target genome list was writen to OceanDNA-b22890/target_genomes.txt
[2023-03-19 00:30:20,184] [INFO] Task started: fastANI
[2023-03-19 00:30:20,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d218bfc-9829-41a9-88fc-267dd7648c12/OceanDNA-b22890.fa --refList OceanDNA-b22890/target_genomes.txt --output OceanDNA-b22890/fastani_result.tsv --threads 1
[2023-03-19 00:30:34,172] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:34,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:30:34,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:30:34,179] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:30:34,179] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:30:34,179] [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
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	79.7979	1102	1762	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	79.6996	1090	1762	95	below_threshold
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	78.5672	810	1762	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	78.4023	816	1762	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	78.3936	814	1762	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	78.3764	818	1762	95	below_threshold
Gimesia aquarii	strain=V144	GCA_007748195.1	2527964	2527964	type	True	77.8824	742	1762	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	77.5492	624	1762	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:30:34,179] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22890/tc_result.tsv
[2023-03-19 00:30:34,179] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:30:34,179] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:30:34,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference/checkm_data
[2023-03-19 00:30:34,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:30:34,219] [INFO] Task started: CheckM
[2023-03-19 00:30:34,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22890/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22890/checkm_input OceanDNA-b22890/checkm_result
[2023-03-19 00:31:53,741] [INFO] Task succeeded: CheckM
[2023-03-19 00:31:53,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:31:53,744] [INFO] ===== Completeness check finished =====
[2023-03-19 00:31:53,745] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:31:53,745] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22890/markers.fasta)
[2023-03-19 00:31:53,746] [INFO] Task started: Blastn
[2023-03-19 00:31:53,746] [INFO] Running command: blastn -query OceanDNA-b22890/markers.fasta -db /var/lib/cwl/stg7e6b1c1c-cf6f-4e84-9b52-65b228347a58/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22890/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:31:54,494] [INFO] Task succeeded: Blastn
[2023-03-19 00:31:54,494] [INFO] Selected 14 target genomes.
[2023-03-19 00:31:54,495] [INFO] Target genome list was writen to OceanDNA-b22890/target_genomes_gtdb.txt
[2023-03-19 00:31:54,521] [INFO] Task started: fastANI
[2023-03-19 00:31:54,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d218bfc-9829-41a9-88fc-267dd7648c12/OceanDNA-b22890.fa --refList OceanDNA-b22890/target_genomes_gtdb.txt --output OceanDNA-b22890/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:32:10,528] [INFO] Task succeeded: fastANI
[2023-03-19 00:32:10,533] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:32:10,534] [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_007744675.1	s__Gimesia alba	79.7907	1103	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754425.1	s__Gimesia fumaroli	79.7039	1089	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746795.1	s__Gimesia algae	78.5622	811	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298035.1	s__Gimesia maris	78.4023	816	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCA_002706765.1	s__Gimesia sp002706765	78.3109	795	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_007748195.1	s__Gimesia aquarii	77.8869	741	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	95.04	95.04	0.88	0.88	2	-
GCF_009720525.1	s__Gimesia benthica	77.5926	642	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_008329715.1	s__Gimesia chilikensis	77.5554	622	1762	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
--------------------------------------------------------------------------------
[2023-03-19 00:32:10,534] [INFO] GTDB search result was written to OceanDNA-b22890/result_gtdb.tsv
[2023-03-19 00:32:10,534] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:32:10,535] [INFO] DFAST_QC result json was written to OceanDNA-b22890/dqc_result.json
[2023-03-19 00:32:10,535] [INFO] DFAST_QC completed!
[2023-03-19 00:32:10,535] [INFO] Total running time: 0h2m25s