[2023-03-19 02:10:16,859] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:10:16,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:10:16,859] [INFO] DQC Reference Directory: /var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference
[2023-03-19 02:10:18,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:10:18,814] [INFO] Task started: Prodigal
[2023-03-19 02:10:18,814] [INFO] Running command: cat /var/lib/cwl/stgcd3bbd2c-fd1e-4f16-808f-9d41f40167cf/OceanDNA-b3023.fa | prodigal -d OceanDNA-b3023/cds.fna -a OceanDNA-b3023/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:10:23,844] [INFO] Task succeeded: Prodigal
[2023-03-19 02:10:23,845] [INFO] Task started: HMMsearch
[2023-03-19 02:10:23,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b3023/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference/reference_markers.hmm OceanDNA-b3023/protein.faa > /dev/null
[2023-03-19 02:10:23,993] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:10:23,993] [INFO] Found 6/6 markers.
[2023-03-19 02:10:24,002] [INFO] Query marker FASTA was written to OceanDNA-b3023/markers.fasta
[2023-03-19 02:10:24,003] [INFO] Task started: Blastn
[2023-03-19 02:10:24,003] [INFO] Running command: blastn -query OceanDNA-b3023/markers.fasta -db /var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference/reference_markers.fasta -out OceanDNA-b3023/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:24,596] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:24,597] [INFO] Selected 21 target genomes.
[2023-03-19 02:10:24,597] [INFO] Target genome list was writen to OceanDNA-b3023/target_genomes.txt
[2023-03-19 02:10:24,641] [INFO] Task started: fastANI
[2023-03-19 02:10:24,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd3bbd2c-fd1e-4f16-808f-9d41f40167cf/OceanDNA-b3023.fa --refList OceanDNA-b3023/target_genomes.txt --output OceanDNA-b3023/fastani_result.tsv --threads 1
[2023-03-19 02:10:34,425] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:34,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:10:34,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:10:34,426] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:10:34,426] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:10:34,426] [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
--------------------------------------------------------------------------------
[2023-03-19 02:10:34,426] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3023/tc_result.tsv
[2023-03-19 02:10:34,426] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:10:34,426] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:10:34,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference/checkm_data
[2023-03-19 02:10:34,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:10:34,618] [INFO] Task started: CheckM
[2023-03-19 02:10:34,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3023/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3023/checkm_input OceanDNA-b3023/checkm_result
[2023-03-19 02:10:53,019] [INFO] Task succeeded: CheckM
[2023-03-19 02:10:53,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:10:53,021] [INFO] ===== Completeness check finished =====
[2023-03-19 02:10:53,022] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:10:53,022] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3023/markers.fasta)
[2023-03-19 02:10:53,022] [INFO] Task started: Blastn
[2023-03-19 02:10:53,022] [INFO] Running command: blastn -query OceanDNA-b3023/markers.fasta -db /var/lib/cwl/stge8630dfa-97cd-402a-aeff-e956e3849a99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3023/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:53,922] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:53,922] [INFO] Selected 7 target genomes.
[2023-03-19 02:10:53,923] [INFO] Target genome list was writen to OceanDNA-b3023/target_genomes_gtdb.txt
[2023-03-19 02:10:54,006] [INFO] Task started: fastANI
[2023-03-19 02:10:54,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd3bbd2c-fd1e-4f16-808f-9d41f40167cf/OceanDNA-b3023.fa --refList OceanDNA-b3023/target_genomes_gtdb.txt --output OceanDNA-b3023/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:10:55,458] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:55,463] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:10:55,463] [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_003569145.1	s__MAG-120802 sp003569145	90.8437	249	304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	99.02	99.02	0.96	0.96	2	-
GCA_016870795.1	s__MAG-120802 sp016870795	90.792	240	304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777515.1	s__MAG-120802 sp005777515	88.6728	189	304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.53	98.39	0.77	0.76	3	-
GCA_002347935.1	s__MAG-120802 sp002347935	87.2647	210	304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.96	98.66	0.86	0.80	28	-
GCA_016870365.1	s__MAG-120802 sp016870365	82.0659	234	304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882885.1	s__MAG-120802 sp018882885	77.6557	87	304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:10:55,463] [INFO] GTDB search result was written to OceanDNA-b3023/result_gtdb.tsv
[2023-03-19 02:10:55,463] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:10:55,464] [INFO] DFAST_QC result json was written to OceanDNA-b3023/dqc_result.json
[2023-03-19 02:10:55,464] [INFO] DFAST_QC completed!
[2023-03-19 02:10:55,464] [INFO] Total running time: 0h0m39s