[2023-03-17 23:54:11,282] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:54:11,282] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:54:11,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference
[2023-03-17 23:54:13,839] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:54:13,840] [INFO] Task started: Prodigal
[2023-03-17 23:54:13,840] [INFO] Running command: cat /var/lib/cwl/stgf4db6ad3-cc21-4533-9a2f-c8c9d1a07702/OceanDNA-b22327.fa | prodigal -d OceanDNA-b22327/cds.fna -a OceanDNA-b22327/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:54:27,634] [INFO] Task succeeded: Prodigal
[2023-03-17 23:54:27,634] [INFO] Task started: HMMsearch
[2023-03-17 23:54:27,634] [INFO] Running command: hmmsearch --tblout OceanDNA-b22327/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference/reference_markers.hmm OceanDNA-b22327/protein.faa > /dev/null
[2023-03-17 23:54:27,835] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:54:27,836] [INFO] Found 6/6 markers.
[2023-03-17 23:54:27,859] [INFO] Query marker FASTA was written to OceanDNA-b22327/markers.fasta
[2023-03-17 23:54:27,860] [INFO] Task started: Blastn
[2023-03-17 23:54:27,860] [INFO] Running command: blastn -query OceanDNA-b22327/markers.fasta -db /var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference/reference_markers.fasta -out OceanDNA-b22327/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:28,419] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:28,423] [INFO] Selected 8 target genomes.
[2023-03-17 23:54:28,423] [INFO] Target genome list was writen to OceanDNA-b22327/target_genomes.txt
[2023-03-17 23:54:28,427] [INFO] Task started: fastANI
[2023-03-17 23:54:28,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4db6ad3-cc21-4533-9a2f-c8c9d1a07702/OceanDNA-b22327.fa --refList OceanDNA-b22327/target_genomes.txt --output OceanDNA-b22327/fastani_result.tsv --threads 1
[2023-03-17 23:54:35,868] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:35,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:54:35,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:54:35,875] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:54:35,876] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:54:35,876] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	78.3875	245	711	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	78.1466	236	711	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	77.8786	219	711	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	77.8154	184	711	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	77.5824	191	711	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	77.2388	152	711	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	75.8545	60	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:54:35,877] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22327/tc_result.tsv
[2023-03-17 23:54:35,877] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:54:35,878] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:54:35,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference/checkm_data
[2023-03-17 23:54:35,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:54:35,884] [INFO] Task started: CheckM
[2023-03-17 23:54:35,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22327/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22327/checkm_input OceanDNA-b22327/checkm_result
[2023-03-17 23:55:13,083] [INFO] Task succeeded: CheckM
[2023-03-17 23:55:13,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.51%
Contamintation: 3.12%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 23:55:13,094] [INFO] ===== Completeness check finished =====
[2023-03-17 23:55:13,094] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:55:13,094] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22327/markers.fasta)
[2023-03-17 23:55:13,095] [INFO] Task started: Blastn
[2023-03-17 23:55:13,095] [INFO] Running command: blastn -query OceanDNA-b22327/markers.fasta -db /var/lib/cwl/stg7a6e718b-8103-4bb9-822b-e255e84b0174/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22327/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:55:13,943] [INFO] Task succeeded: Blastn
[2023-03-17 23:55:13,944] [INFO] Selected 13 target genomes.
[2023-03-17 23:55:13,944] [INFO] Target genome list was writen to OceanDNA-b22327/target_genomes_gtdb.txt
[2023-03-17 23:55:13,958] [INFO] Task started: fastANI
[2023-03-17 23:55:13,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4db6ad3-cc21-4533-9a2f-c8c9d1a07702/OceanDNA-b22327.fa --refList OceanDNA-b22327/target_genomes_gtdb.txt --output OceanDNA-b22327/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:55:23,210] [INFO] Task succeeded: fastANI
[2023-03-17 23:55:23,216] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:55:23,216] [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
GCA_007745835.1	s__Botrimarina sp007745835	78.4921	270	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	78.4522	241	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	78.1666	234	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	77.9046	218	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCF_007859765.1	s__Posidoniimonas corsicana	77.8681	181	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	77.6003	189	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859815.1	s__Botrimarina hoheduenensis	77.2574	151	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.9684	56	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405515.1	s__UBA4655 sp002405515	75.4081	56	711	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA4655	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:55:23,217] [INFO] GTDB search result was written to OceanDNA-b22327/result_gtdb.tsv
[2023-03-17 23:55:23,217] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:55:23,218] [INFO] DFAST_QC result json was written to OceanDNA-b22327/dqc_result.json
[2023-03-17 23:55:23,218] [INFO] DFAST_QC completed!
[2023-03-17 23:55:23,218] [INFO] Total running time: 0h1m12s