[2023-03-16 08:58:01,983] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:58:01,984] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:58:01,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference
[2023-03-16 08:58:03,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:58:03,122] [INFO] Task started: Prodigal
[2023-03-16 08:58:03,122] [INFO] Running command: cat /var/lib/cwl/stg3f3ff3c0-fad1-4e7f-be98-c16f33f46d44/OceanDNA-b19928.fa | prodigal -d OceanDNA-b19928/cds.fna -a OceanDNA-b19928/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:58:13,040] [INFO] Task succeeded: Prodigal
[2023-03-16 08:58:13,041] [INFO] Task started: HMMsearch
[2023-03-16 08:58:13,041] [INFO] Running command: hmmsearch --tblout OceanDNA-b19928/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference/reference_markers.hmm OceanDNA-b19928/protein.faa > /dev/null
[2023-03-16 08:58:13,206] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:58:13,207] [INFO] Found 6/6 markers.
[2023-03-16 08:58:13,224] [INFO] Query marker FASTA was written to OceanDNA-b19928/markers.fasta
[2023-03-16 08:58:13,225] [INFO] Task started: Blastn
[2023-03-16 08:58:13,225] [INFO] Running command: blastn -query OceanDNA-b19928/markers.fasta -db /var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference/reference_markers.fasta -out OceanDNA-b19928/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:58:13,733] [INFO] Task succeeded: Blastn
[2023-03-16 08:58:13,735] [INFO] Selected 16 target genomes.
[2023-03-16 08:58:13,735] [INFO] Target genome list was writen to OceanDNA-b19928/target_genomes.txt
[2023-03-16 08:58:13,743] [INFO] Task started: fastANI
[2023-03-16 08:58:13,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3ff3c0-fad1-4e7f-be98-c16f33f46d44/OceanDNA-b19928.fa --refList OceanDNA-b19928/target_genomes.txt --output OceanDNA-b19928/fastani_result.tsv --threads 1
[2023-03-16 08:58:24,631] [INFO] Task succeeded: fastANI
[2023-03-16 08:58:24,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:58:24,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:58:24,632] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:58:24,632] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:58:24,632] [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
--------------------------------------------------------------------------------
[2023-03-16 08:58:24,632] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19928/tc_result.tsv
[2023-03-16 08:58:24,633] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:58:24,633] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:58:24,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference/checkm_data
[2023-03-16 08:58:24,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:58:24,640] [INFO] Task started: CheckM
[2023-03-16 08:58:24,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19928/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19928/checkm_input OceanDNA-b19928/checkm_result
[2023-03-16 08:58:54,337] [INFO] Task succeeded: CheckM
[2023-03-16 08:58:54,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.77%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:58:54,340] [INFO] ===== Completeness check finished =====
[2023-03-16 08:58:54,340] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:58:54,340] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19928/markers.fasta)
[2023-03-16 08:58:54,340] [INFO] Task started: Blastn
[2023-03-16 08:58:54,340] [INFO] Running command: blastn -query OceanDNA-b19928/markers.fasta -db /var/lib/cwl/stg59b5b98d-91d2-4f2c-ba65-b2c200b5f30b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19928/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:58:55,054] [INFO] Task succeeded: Blastn
[2023-03-16 08:58:55,055] [INFO] Selected 17 target genomes.
[2023-03-16 08:58:55,055] [INFO] Target genome list was writen to OceanDNA-b19928/target_genomes_gtdb.txt
[2023-03-16 08:58:55,069] [INFO] Task started: fastANI
[2023-03-16 08:58:55,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3ff3c0-fad1-4e7f-be98-c16f33f46d44/OceanDNA-b19928.fa --refList OceanDNA-b19928/target_genomes_gtdb.txt --output OceanDNA-b19928/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:59:02,365] [INFO] Task succeeded: fastANI
[2023-03-16 08:59:02,371] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:59:02,371] [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_015658495.1	s__GCA-2722105 sp015658495	98.1147	301	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018692355.1	s__GCA-2722105 sp018692355	81.5988	289	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.23	99.02	0.79	0.73	14	-
GCA_018674095.1	s__GCA-2722105 sp018674095	78.5624	191	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
GCA_018649625.1	s__GCA-2722105 sp018649625	77.5488	122	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
GCA_002722105.1	s__GCA-2722105 sp002722105	75.9876	67	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:59:02,371] [INFO] GTDB search result was written to OceanDNA-b19928/result_gtdb.tsv
[2023-03-16 08:59:02,371] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:59:02,372] [INFO] DFAST_QC result json was written to OceanDNA-b19928/dqc_result.json
[2023-03-16 08:59:02,372] [INFO] DFAST_QC completed!
[2023-03-16 08:59:02,372] [INFO] Total running time: 0h1m0s