[2023-03-15 10:49:28,599] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference
[2023-03-15 10:49:29,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,730] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,731] [INFO] Running command: cat /var/lib/cwl/stg13948126-6150-4bf5-97f9-833d05dccf24/OceanDNA-b45492.fa | prodigal -d OceanDNA-b45492/cds.fna -a OceanDNA-b45492/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:50,635] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:50,635] [INFO] Task started: HMMsearch
[2023-03-15 10:49:50,635] [INFO] Running command: hmmsearch --tblout OceanDNA-b45492/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference/reference_markers.hmm OceanDNA-b45492/protein.faa > /dev/null
[2023-03-15 10:49:50,869] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:50,870] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13948126-6150-4bf5-97f9-833d05dccf24/OceanDNA-b45492.fa]
[2023-03-15 10:49:50,895] [INFO] Query marker FASTA was written to OceanDNA-b45492/markers.fasta
[2023-03-15 10:49:50,906] [INFO] Task started: Blastn
[2023-03-15 10:49:50,907] [INFO] Running command: blastn -query OceanDNA-b45492/markers.fasta -db /var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference/reference_markers.fasta -out OceanDNA-b45492/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:51,527] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:51,528] [INFO] Selected 11 target genomes.
[2023-03-15 10:49:51,528] [INFO] Target genome list was writen to OceanDNA-b45492/target_genomes.txt
[2023-03-15 10:49:51,536] [INFO] Task started: fastANI
[2023-03-15 10:49:51,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg13948126-6150-4bf5-97f9-833d05dccf24/OceanDNA-b45492.fa --refList OceanDNA-b45492/target_genomes.txt --output OceanDNA-b45492/fastani_result.tsv --threads 1
[2023-03-15 10:49:57,577] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:57,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:57,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:57,578] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:57,578] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:57,578] [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
--------------------------------------------------------------------------------
[2023-03-15 10:49:57,579] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45492/tc_result.tsv
[2023-03-15 10:49:57,579] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:57,579] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:57,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference/checkm_data
[2023-03-15 10:49:57,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:57,588] [INFO] Task started: CheckM
[2023-03-15 10:49:57,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45492/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45492/checkm_input OceanDNA-b45492/checkm_result
[2023-03-15 10:50:52,944] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:52,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:52,948] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:52,948] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:52,948] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45492/markers.fasta)
[2023-03-15 10:50:52,949] [INFO] Task started: Blastn
[2023-03-15 10:50:52,949] [INFO] Running command: blastn -query OceanDNA-b45492/markers.fasta -db /var/lib/cwl/stg953e8ee3-60aa-47f0-864d-a4495a27ba99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45492/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:53,675] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:53,676] [INFO] Selected 23 target genomes.
[2023-03-15 10:50:53,676] [INFO] Target genome list was writen to OceanDNA-b45492/target_genomes_gtdb.txt
[2023-03-15 10:50:53,702] [INFO] Task started: fastANI
[2023-03-15 10:50:53,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg13948126-6150-4bf5-97f9-833d05dccf24/OceanDNA-b45492.fa --refList OceanDNA-b45492/target_genomes_gtdb.txt --output OceanDNA-b45492/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:51:04,323] [INFO] Task succeeded: fastANI
[2023-03-15 10:51:04,327] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:51:04,327] [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_002721705.1	s__UBA2993 sp002721705	78.2497	74	690	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__UBA2993	95.0	99.38	99.15	0.85	0.79	3	-
GCA_018695085.1	s__GCA-2730975 sp018695085	77.3723	64	690	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	98.14	98.04	0.72	0.68	4	-
GCA_002730975.1	s__GCA-2730975 sp002730975	77.1017	78	690	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	99.68	99.68	0.85	0.85	2	-
GCA_002500665.1	s__MB11C04 sp002500665	77.0409	54	690	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
--------------------------------------------------------------------------------
[2023-03-15 10:51:04,327] [INFO] GTDB search result was written to OceanDNA-b45492/result_gtdb.tsv
[2023-03-15 10:51:04,327] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:51:04,328] [INFO] DFAST_QC result json was written to OceanDNA-b45492/dqc_result.json
[2023-03-15 10:51:04,328] [INFO] DFAST_QC completed!
[2023-03-15 10:51:04,328] [INFO] Total running time: 0h1m36s