[2023-03-17 13:01:51,397] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,398] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,398] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference
[2023-03-17 13:01:52,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,658] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,658] [INFO] Running command: cat /var/lib/cwl/stg7bceac8d-5fa2-444e-b59d-5215f9b3f23e/OceanDNA-b18640.fa | prodigal -d OceanDNA-b18640/cds.fna -a OceanDNA-b18640/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:01:57,704] [INFO] Task succeeded: Prodigal
[2023-03-17 13:01:57,704] [INFO] Task started: HMMsearch
[2023-03-17 13:01:57,704] [INFO] Running command: hmmsearch --tblout OceanDNA-b18640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference/reference_markers.hmm OceanDNA-b18640/protein.faa > /dev/null
[2023-03-17 13:01:57,854] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:01:57,854] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7bceac8d-5fa2-444e-b59d-5215f9b3f23e/OceanDNA-b18640.fa]
[2023-03-17 13:01:57,866] [INFO] Query marker FASTA was written to OceanDNA-b18640/markers.fasta
[2023-03-17 13:01:57,866] [INFO] Task started: Blastn
[2023-03-17 13:01:57,866] [INFO] Running command: blastn -query OceanDNA-b18640/markers.fasta -db /var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference/reference_markers.fasta -out OceanDNA-b18640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:01:58,330] [INFO] Task succeeded: Blastn
[2023-03-17 13:01:58,331] [INFO] Selected 5 target genomes.
[2023-03-17 13:01:58,331] [INFO] Target genome list was writen to OceanDNA-b18640/target_genomes.txt
[2023-03-17 13:01:58,334] [INFO] Task started: fastANI
[2023-03-17 13:01:58,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bceac8d-5fa2-444e-b59d-5215f9b3f23e/OceanDNA-b18640.fa --refList OceanDNA-b18640/target_genomes.txt --output OceanDNA-b18640/fastani_result.tsv --threads 1
[2023-03-17 13:02:00,376] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:00,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:00,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:00,377] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:00,377] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:00,377] [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
--------------------------------------------------------------------------------
[2023-03-17 13:02:00,377] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18640/tc_result.tsv
[2023-03-17 13:02:00,377] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:00,377] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:00,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference/checkm_data
[2023-03-17 13:02:00,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:00,382] [INFO] Task started: CheckM
[2023-03-17 13:02:00,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18640/checkm_input OceanDNA-b18640/checkm_result
[2023-03-17 13:02:19,375] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:19,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.30%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:19,378] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:19,378] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:19,378] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18640/markers.fasta)
[2023-03-17 13:02:19,378] [INFO] Task started: Blastn
[2023-03-17 13:02:19,378] [INFO] Running command: blastn -query OceanDNA-b18640/markers.fasta -db /var/lib/cwl/stgf2a2bbd3-fb3d-42ce-abcc-5ee2e88b5b99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:19,787] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:19,788] [INFO] Selected 15 target genomes.
[2023-03-17 13:02:19,788] [INFO] Target genome list was writen to OceanDNA-b18640/target_genomes_gtdb.txt
[2023-03-17 13:02:20,380] [INFO] Task started: fastANI
[2023-03-17 13:02:20,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bceac8d-5fa2-444e-b59d-5215f9b3f23e/OceanDNA-b18640.fa --refList OceanDNA-b18640/target_genomes_gtdb.txt --output OceanDNA-b18640/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:24,138] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:24,141] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:02:24,141] [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_004321715.1	s__GCA-002701945 sp004321715	87.7138	204	299	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701785.1	s__GCA-002701945 sp002701785	87.149	261	299	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	97.49	97.49	0.87	0.87	2	-
GCA_002701945.1	s__GCA-002701945 sp002701945	80.8223	196	299	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:24,141] [INFO] GTDB search result was written to OceanDNA-b18640/result_gtdb.tsv
[2023-03-17 13:02:24,141] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:24,142] [INFO] DFAST_QC result json was written to OceanDNA-b18640/dqc_result.json
[2023-03-17 13:02:24,142] [INFO] DFAST_QC completed!
[2023-03-17 13:02:24,142] [INFO] Total running time: 0h0m33s