[2023-03-18 23:11:06,912] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,912] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference
[2023-03-18 23:11:08,148] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,148] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,148] [INFO] Running command: cat /var/lib/cwl/stg9d68c38e-ff17-499f-8957-72c0075cfa5b/OceanDNA-b19120.fa | prodigal -d OceanDNA-b19120/cds.fna -a OceanDNA-b19120/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:14,476] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:14,477] [INFO] Task started: HMMsearch
[2023-03-18 23:11:14,477] [INFO] Running command: hmmsearch --tblout OceanDNA-b19120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference/reference_markers.hmm OceanDNA-b19120/protein.faa > /dev/null
[2023-03-18 23:11:14,674] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:14,675] [INFO] Found 6/6 markers.
[2023-03-18 23:11:14,687] [INFO] Query marker FASTA was written to OceanDNA-b19120/markers.fasta
[2023-03-18 23:11:14,687] [INFO] Task started: Blastn
[2023-03-18 23:11:14,687] [INFO] Running command: blastn -query OceanDNA-b19120/markers.fasta -db /var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference/reference_markers.fasta -out OceanDNA-b19120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:15,205] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:15,206] [INFO] Selected 19 target genomes.
[2023-03-18 23:11:15,206] [INFO] Target genome list was writen to OceanDNA-b19120/target_genomes.txt
[2023-03-18 23:11:15,218] [INFO] Task started: fastANI
[2023-03-18 23:11:15,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d68c38e-ff17-499f-8957-72c0075cfa5b/OceanDNA-b19120.fa --refList OceanDNA-b19120/target_genomes.txt --output OceanDNA-b19120/fastani_result.tsv --threads 1
[2023-03-18 23:11:23,145] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:23,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:23,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:23,146] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:23,146] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:23,146] [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 23:11:23,146] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19120/tc_result.tsv
[2023-03-18 23:11:23,146] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:23,146] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:23,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference/checkm_data
[2023-03-18 23:11:23,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:23,151] [INFO] Task started: CheckM
[2023-03-18 23:11:23,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19120/checkm_input OceanDNA-b19120/checkm_result
[2023-03-18 23:11:45,257] [INFO] Task succeeded: CheckM
[2023-03-18 23:11:45,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 3.24%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:11:45,260] [INFO] ===== Completeness check finished =====
[2023-03-18 23:11:45,260] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:11:45,260] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19120/markers.fasta)
[2023-03-18 23:11:45,260] [INFO] Task started: Blastn
[2023-03-18 23:11:45,260] [INFO] Running command: blastn -query OceanDNA-b19120/markers.fasta -db /var/lib/cwl/stg9063e4a6-ff08-4c3a-a33a-b8b4aec3564d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:46,001] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:46,002] [INFO] Selected 20 target genomes.
[2023-03-18 23:11:46,002] [INFO] Target genome list was writen to OceanDNA-b19120/target_genomes_gtdb.txt
[2023-03-18 23:11:46,023] [INFO] Task started: fastANI
[2023-03-18 23:11:46,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d68c38e-ff17-499f-8957-72c0075cfa5b/OceanDNA-b19120.fa --refList OceanDNA-b19120/target_genomes_gtdb.txt --output OceanDNA-b19120/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:11:52,505] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:52,509] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:11:52,510] [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_014239505.1	s__TCS55 sp014239505	98.31	319	410	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	98.16	97.99	0.75	0.73	6	conclusive
GCA_905182385.1	s__TCS55 sp905182385	83.3296	257	410	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	77.5827	61	410	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_002701875.1	s__GCA-002713455 sp002701875	76.5757	59	410	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_902581045.1	s__GCA-002713455 sp902581045	76.3888	52	410	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002713455	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:11:52,510] [INFO] GTDB search result was written to OceanDNA-b19120/result_gtdb.tsv
[2023-03-18 23:11:52,510] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:11:52,511] [INFO] DFAST_QC result json was written to OceanDNA-b19120/dqc_result.json
[2023-03-18 23:11:52,511] [INFO] DFAST_QC completed!
[2023-03-18 23:11:52,511] [INFO] Total running time: 0h0m46s