[2023-03-18 01:26:26,397] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,397] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference
[2023-03-18 01:26:27,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,623] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,623] [INFO] Running command: cat /var/lib/cwl/stg90969830-d779-4edc-8907-5a7e15145781/OceanDNA-b19147.fa | prodigal -d OceanDNA-b19147/cds.fna -a OceanDNA-b19147/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:35,493] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:35,493] [INFO] Task started: HMMsearch
[2023-03-18 01:26:35,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b19147/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference/reference_markers.hmm OceanDNA-b19147/protein.faa > /dev/null
[2023-03-18 01:26:35,695] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:35,698] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90969830-d779-4edc-8907-5a7e15145781/OceanDNA-b19147.fa]
[2023-03-18 01:26:35,712] [INFO] Query marker FASTA was written to OceanDNA-b19147/markers.fasta
[2023-03-18 01:26:35,713] [INFO] Task started: Blastn
[2023-03-18 01:26:35,713] [INFO] Running command: blastn -query OceanDNA-b19147/markers.fasta -db /var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference/reference_markers.fasta -out OceanDNA-b19147/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:36,271] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:36,272] [INFO] Selected 20 target genomes.
[2023-03-18 01:26:36,272] [INFO] Target genome list was writen to OceanDNA-b19147/target_genomes.txt
[2023-03-18 01:26:36,307] [INFO] Task started: fastANI
[2023-03-18 01:26:36,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg90969830-d779-4edc-8907-5a7e15145781/OceanDNA-b19147.fa --refList OceanDNA-b19147/target_genomes.txt --output OceanDNA-b19147/fastani_result.tsv --threads 1
[2023-03-18 01:26:50,450] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:50,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:50,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:50,451] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:50,451] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:50,451] [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 01:26:50,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19147/tc_result.tsv
[2023-03-18 01:26:50,451] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:50,451] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:50,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference/checkm_data
[2023-03-18 01:26:50,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:50,457] [INFO] Task started: CheckM
[2023-03-18 01:26:50,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19147/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19147/checkm_input OceanDNA-b19147/checkm_result
[2023-03-18 01:27:16,426] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:16,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:16,428] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:16,428] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:16,429] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19147/markers.fasta)
[2023-03-18 01:27:16,429] [INFO] Task started: Blastn
[2023-03-18 01:27:16,429] [INFO] Running command: blastn -query OceanDNA-b19147/markers.fasta -db /var/lib/cwl/stg3ef749a5-9de1-44f8-9c4c-c342bc43d003/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19147/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:17,109] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:17,110] [INFO] Selected 20 target genomes.
[2023-03-18 01:27:17,110] [INFO] Target genome list was writen to OceanDNA-b19147/target_genomes_gtdb.txt
[2023-03-18 01:27:17,185] [INFO] Task started: fastANI
[2023-03-18 01:27:17,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg90969830-d779-4edc-8907-5a7e15145781/OceanDNA-b19147.fa --refList OceanDNA-b19147/target_genomes_gtdb.txt --output OceanDNA-b19147/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:27,184] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:27,188] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:27:27,189] [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_002471845.1	s__TCS55 sp002471845	99.9184	405	446	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.96	99.93	0.96	0.96	5	conclusive
GCA_012964665.1	s__TCS55 sp012964665	79.7114	117	446	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.32	99.03	0.83	0.81	3	-
GCA_002716525.1	s__TCS55 sp002716525	79.4155	75	446	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674655.1	s__TCS55 sp018674655	78.8911	123	446	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_018647265.1	s__TCS55 sp018647265	78.072	151	446	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.87	99.79	0.92	0.89	15	-
GCA_014382015.1	s__TCS55 sp014382015	77.2828	108	446	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.95	99.95	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:27,189] [INFO] GTDB search result was written to OceanDNA-b19147/result_gtdb.tsv
[2023-03-18 01:27:27,189] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:27,190] [INFO] DFAST_QC result json was written to OceanDNA-b19147/dqc_result.json
[2023-03-18 01:27:27,190] [INFO] DFAST_QC completed!
[2023-03-18 01:27:27,190] [INFO] Total running time: 0h1m1s