[2023-03-18 10:27:56,316] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:27:56,319] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:27:56,319] [INFO] DQC Reference Directory: /var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference
[2023-03-18 10:27:57,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:27:57,422] [INFO] Task started: Prodigal
[2023-03-18 10:27:57,422] [INFO] Running command: cat /var/lib/cwl/stg23c70940-6371-4c6a-834e-8cf90ce59ce1/OceanDNA-b19065.fa | prodigal -d OceanDNA-b19065/cds.fna -a OceanDNA-b19065/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:28:05,408] [INFO] Task succeeded: Prodigal
[2023-03-18 10:28:05,408] [INFO] Task started: HMMsearch
[2023-03-18 10:28:05,408] [INFO] Running command: hmmsearch --tblout OceanDNA-b19065/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference/reference_markers.hmm OceanDNA-b19065/protein.faa > /dev/null
[2023-03-18 10:28:05,578] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:28:05,579] [INFO] Found 6/6 markers.
[2023-03-18 10:28:05,649] [INFO] Query marker FASTA was written to OceanDNA-b19065/markers.fasta
[2023-03-18 10:28:05,650] [INFO] Task started: Blastn
[2023-03-18 10:28:05,650] [INFO] Running command: blastn -query OceanDNA-b19065/markers.fasta -db /var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference/reference_markers.fasta -out OceanDNA-b19065/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:28:06,169] [INFO] Task succeeded: Blastn
[2023-03-18 10:28:06,189] [INFO] Selected 20 target genomes.
[2023-03-18 10:28:06,190] [INFO] Target genome list was writen to OceanDNA-b19065/target_genomes.txt
[2023-03-18 10:28:06,199] [INFO] Task started: fastANI
[2023-03-18 10:28:06,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c70940-6371-4c6a-834e-8cf90ce59ce1/OceanDNA-b19065.fa --refList OceanDNA-b19065/target_genomes.txt --output OceanDNA-b19065/fastani_result.tsv --threads 1
[2023-03-18 10:28:17,218] [INFO] Task succeeded: fastANI
[2023-03-18 10:28:17,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:28:17,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:28:17,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:28:17,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:28:17,219] [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
--------------------------------------------------------------------------------
[2023-03-18 10:28:17,226] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19065/tc_result.tsv
[2023-03-18 10:28:17,239] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:28:17,239] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:28:17,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference/checkm_data
[2023-03-18 10:28:17,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:28:17,251] [INFO] Task started: CheckM
[2023-03-18 10:28:17,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19065/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19065/checkm_input OceanDNA-b19065/checkm_result
[2023-03-18 10:28:42,261] [INFO] Task succeeded: CheckM
[2023-03-18 10:28:42,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:28:42,332] [INFO] ===== Completeness check finished =====
[2023-03-18 10:28:42,332] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:28:42,332] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19065/markers.fasta)
[2023-03-18 10:28:42,333] [INFO] Task started: Blastn
[2023-03-18 10:28:42,333] [INFO] Running command: blastn -query OceanDNA-b19065/markers.fasta -db /var/lib/cwl/stge18fb809-008e-4cd1-be11-41b992386a37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19065/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:28:43,063] [INFO] Task succeeded: Blastn
[2023-03-18 10:28:43,083] [INFO] Selected 22 target genomes.
[2023-03-18 10:28:43,083] [INFO] Target genome list was writen to OceanDNA-b19065/target_genomes_gtdb.txt
[2023-03-18 10:28:43,216] [INFO] Task started: fastANI
[2023-03-18 10:28:43,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c70940-6371-4c6a-834e-8cf90ce59ce1/OceanDNA-b19065.fa --refList OceanDNA-b19065/target_genomes_gtdb.txt --output OceanDNA-b19065/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:28:50,335] [INFO] Task succeeded: fastANI
[2023-03-18 10:28:50,339] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:28:50,340] [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_905182385.1	s__TCS55 sp905182385	86.8533	302	516	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239505.1	s__TCS55 sp014239505	83.9146	315	516	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	98.16	97.99	0.75	0.73	6	-
GCA_002701875.1	s__GCA-002713455 sp002701875	76.7707	63	516	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002713455	95.0	98.93	98.93	0.84	0.84	2	-
GCA_001577025.1	s__TCS55 sp001577025	76.7333	52	516	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	95.80	95.01	0.79	0.74	7	-
GCA_018674655.1	s__TCS55 sp018674655	76.5872	73	516	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_016845785.1	s__TCS55 sp016845785	76.1361	56	516	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:28:50,348] [INFO] GTDB search result was written to OceanDNA-b19065/result_gtdb.tsv
[2023-03-18 10:28:50,363] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:28:50,372] [INFO] DFAST_QC result json was written to OceanDNA-b19065/dqc_result.json
[2023-03-18 10:28:50,372] [INFO] DFAST_QC completed!
[2023-03-18 10:28:50,372] [INFO] Total running time: 0h0m54s