[2023-03-16 08:02:40,396] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:02:40,396] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:02:40,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference
[2023-03-16 08:02:41,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:02:41,599] [INFO] Task started: Prodigal
[2023-03-16 08:02:41,599] [INFO] Running command: cat /var/lib/cwl/stg53d66916-fee3-4bca-a9c0-2708406f062d/OceanDNA-a1755.fa | prodigal -d OceanDNA-a1755/cds.fna -a OceanDNA-a1755/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:02:49,549] [INFO] Task succeeded: Prodigal
[2023-03-16 08:02:49,549] [INFO] Task started: HMMsearch
[2023-03-16 08:02:49,549] [INFO] Running command: hmmsearch --tblout OceanDNA-a1755/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference/reference_markers.hmm OceanDNA-a1755/protein.faa > /dev/null
[2023-03-16 08:02:49,689] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:02:49,690] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg53d66916-fee3-4bca-a9c0-2708406f062d/OceanDNA-a1755.fa]
[2023-03-16 08:02:49,716] [INFO] Query marker FASTA was written to OceanDNA-a1755/markers.fasta
[2023-03-16 08:02:49,717] [INFO] Task started: Blastn
[2023-03-16 08:02:49,717] [INFO] Running command: blastn -query OceanDNA-a1755/markers.fasta -db /var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference/reference_markers.fasta -out OceanDNA-a1755/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:02:50,205] [INFO] Task succeeded: Blastn
[2023-03-16 08:02:50,209] [INFO] Selected 5 target genomes.
[2023-03-16 08:02:50,209] [INFO] Target genome list was writen to OceanDNA-a1755/target_genomes.txt
[2023-03-16 08:02:50,220] [INFO] Task started: fastANI
[2023-03-16 08:02:50,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d66916-fee3-4bca-a9c0-2708406f062d/OceanDNA-a1755.fa --refList OceanDNA-a1755/target_genomes.txt --output OceanDNA-a1755/fastani_result.tsv --threads 1
[2023-03-16 08:02:52,802] [INFO] Task succeeded: fastANI
[2023-03-16 08:02:52,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:02:52,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:02:52,803] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:02:52,803] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:02:52,803] [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 08:02:52,804] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1755/tc_result.tsv
[2023-03-16 08:02:52,804] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:02:52,805] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:02:52,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference/checkm_data
[2023-03-16 08:02:52,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:02:52,813] [INFO] Task started: CheckM
[2023-03-16 08:02:52,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1755/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1755/checkm_input OceanDNA-a1755/checkm_result
[2023-03-16 08:03:15,050] [INFO] Task succeeded: CheckM
[2023-03-16 08:03:15,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:03:15,229] [INFO] ===== Completeness check finished =====
[2023-03-16 08:03:15,229] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:03:15,229] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1755/markers.fasta)
[2023-03-16 08:03:15,230] [INFO] Task started: Blastn
[2023-03-16 08:03:15,230] [INFO] Running command: blastn -query OceanDNA-a1755/markers.fasta -db /var/lib/cwl/stg61d6d310-1252-40b0-9093-af65a682137e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1755/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:03:15,860] [INFO] Task succeeded: Blastn
[2023-03-16 08:03:15,860] [INFO] Selected 7 target genomes.
[2023-03-16 08:03:15,861] [INFO] Target genome list was writen to OceanDNA-a1755/target_genomes_gtdb.txt
[2023-03-16 08:03:16,052] [INFO] Task started: fastANI
[2023-03-16 08:03:16,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d66916-fee3-4bca-a9c0-2708406f062d/OceanDNA-a1755.fa --refList OceanDNA-a1755/target_genomes_gtdb.txt --output OceanDNA-a1755/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:03:18,146] [INFO] Task succeeded: fastANI
[2023-03-16 08:03:18,150] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:03:18,150] [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_002731655.1	s__UBA8886 sp002731655	99.3085	226	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	95.77	95.71	0.74	0.71	4	conclusive
GCA_003193815.1	s__UBA8886 sp003193815	94.9628	145	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002509165.1	s__UBA8886 sp002509165	91.7352	248	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	99.54	99.45	0.84	0.83	3	-
GCA_002731905.1	s__UBA8886 sp002731905	80.1884	144	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687355.1	s__UBA8886 sp002687355	79.663	114	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	99.48	99.48	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:03:18,150] [INFO] GTDB search result was written to OceanDNA-a1755/result_gtdb.tsv
[2023-03-16 08:03:18,151] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:03:18,153] [INFO] DFAST_QC result json was written to OceanDNA-a1755/dqc_result.json
[2023-03-16 08:03:18,153] [INFO] DFAST_QC completed!
[2023-03-16 08:03:18,153] [INFO] Total running time: 0h0m38s