[2023-03-17 10:48:47,614] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:47,614] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:47,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference
[2023-03-17 10:48:48,800] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:48,801] [INFO] Task started: Prodigal
[2023-03-17 10:48:48,801] [INFO] Running command: cat /var/lib/cwl/stg16a48d1d-0187-4544-9446-731c9cda6439/OceanDNA-b17761.fa | prodigal -d OceanDNA-b17761/cds.fna -a OceanDNA-b17761/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:49:03,208] [INFO] Task succeeded: Prodigal
[2023-03-17 10:49:03,209] [INFO] Task started: HMMsearch
[2023-03-17 10:49:03,209] [INFO] Running command: hmmsearch --tblout OceanDNA-b17761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference/reference_markers.hmm OceanDNA-b17761/protein.faa > /dev/null
[2023-03-17 10:49:03,454] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:49:03,455] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg16a48d1d-0187-4544-9446-731c9cda6439/OceanDNA-b17761.fa]
[2023-03-17 10:49:03,482] [INFO] Query marker FASTA was written to OceanDNA-b17761/markers.fasta
[2023-03-17 10:49:03,483] [INFO] Task started: Blastn
[2023-03-17 10:49:03,483] [INFO] Running command: blastn -query OceanDNA-b17761/markers.fasta -db /var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference/reference_markers.fasta -out OceanDNA-b17761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:04,071] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:04,072] [INFO] Selected 38 target genomes.
[2023-03-17 10:49:04,073] [INFO] Target genome list was writen to OceanDNA-b17761/target_genomes.txt
[2023-03-17 10:49:04,200] [INFO] Task started: fastANI
[2023-03-17 10:49:04,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg16a48d1d-0187-4544-9446-731c9cda6439/OceanDNA-b17761.fa --refList OceanDNA-b17761/target_genomes.txt --output OceanDNA-b17761/fastani_result.tsv --threads 1
[2023-03-17 10:49:36,278] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:36,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:36,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:36,279] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:36,279] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:36,279] [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 10:49:36,489] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17761/tc_result.tsv
[2023-03-17 10:49:36,490] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:36,490] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:36,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference/checkm_data
[2023-03-17 10:49:36,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:36,677] [INFO] Task started: CheckM
[2023-03-17 10:49:36,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17761/checkm_input OceanDNA-b17761/checkm_result
[2023-03-17 10:50:15,487] [INFO] Task succeeded: CheckM
[2023-03-17 10:50:15,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:50:15,490] [INFO] ===== Completeness check finished =====
[2023-03-17 10:50:15,491] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:50:15,491] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17761/markers.fasta)
[2023-03-17 10:50:15,492] [INFO] Task started: Blastn
[2023-03-17 10:50:15,492] [INFO] Running command: blastn -query OceanDNA-b17761/markers.fasta -db /var/lib/cwl/stgcca3ef00-76be-4b9b-a00c-2c9dac413ba7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:50:16,354] [INFO] Task succeeded: Blastn
[2023-03-17 10:50:16,355] [INFO] Selected 28 target genomes.
[2023-03-17 10:50:16,355] [INFO] Target genome list was writen to OceanDNA-b17761/target_genomes_gtdb.txt
[2023-03-17 10:50:16,504] [INFO] Task started: fastANI
[2023-03-17 10:50:16,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg16a48d1d-0187-4544-9446-731c9cda6439/OceanDNA-b17761.fa --refList OceanDNA-b17761/target_genomes_gtdb.txt --output OceanDNA-b17761/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:50:38,014] [INFO] Task succeeded: fastANI
[2023-03-17 10:50:38,020] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:50:38,020] [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_002726335.1	s__UBA8231 sp002726335	79.6151	406	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725915.1	s__GCA-2725915 sp002725915	76.8865	76	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712305.1	s__UBA12574 sp002712305	76.3424	86	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	-
GCA_018673255.1	s__UBA12574 sp018673255	76.1118	106	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	76.0911	71	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187725.1	s__SICG01 sp016187725	76.0488	74	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691525.1	s__SICG01 sp009691525	75.997	54	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867395.1	s__SICG01 sp016867395	75.9895	75	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660835.1	s__UBA12574 sp018660835	75.7504	72	676	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	99.93	99.91	0.98	0.97	7	-
--------------------------------------------------------------------------------
[2023-03-17 10:50:38,021] [INFO] GTDB search result was written to OceanDNA-b17761/result_gtdb.tsv
[2023-03-17 10:50:38,021] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:50:38,022] [INFO] DFAST_QC result json was written to OceanDNA-b17761/dqc_result.json
[2023-03-17 10:50:38,022] [INFO] DFAST_QC completed!
[2023-03-17 10:50:38,022] [INFO] Total running time: 0h1m50s