[2023-03-17 03:24:50,934] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,935] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference
[2023-03-17 03:24:52,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,004] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,004] [INFO] Running command: cat /var/lib/cwl/stg3e9d0618-48be-4001-9612-4538413f02b7/OceanDNA-b20548.fa | prodigal -d OceanDNA-b20548/cds.fna -a OceanDNA-b20548/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:24:57,757] [INFO] Task succeeded: Prodigal
[2023-03-17 03:24:57,757] [INFO] Task started: HMMsearch
[2023-03-17 03:24:57,757] [INFO] Running command: hmmsearch --tblout OceanDNA-b20548/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference/reference_markers.hmm OceanDNA-b20548/protein.faa > /dev/null
[2023-03-17 03:24:57,931] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:24:57,931] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3e9d0618-48be-4001-9612-4538413f02b7/OceanDNA-b20548.fa]
[2023-03-17 03:24:57,951] [INFO] Query marker FASTA was written to OceanDNA-b20548/markers.fasta
[2023-03-17 03:24:57,951] [INFO] Task started: Blastn
[2023-03-17 03:24:57,951] [INFO] Running command: blastn -query OceanDNA-b20548/markers.fasta -db /var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference/reference_markers.fasta -out OceanDNA-b20548/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:24:58,490] [INFO] Task succeeded: Blastn
[2023-03-17 03:24:58,491] [INFO] Selected 17 target genomes.
[2023-03-17 03:24:58,491] [INFO] Target genome list was writen to OceanDNA-b20548/target_genomes.txt
[2023-03-17 03:24:58,501] [INFO] Task started: fastANI
[2023-03-17 03:24:58,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e9d0618-48be-4001-9612-4538413f02b7/OceanDNA-b20548.fa --refList OceanDNA-b20548/target_genomes.txt --output OceanDNA-b20548/fastani_result.tsv --threads 1
[2023-03-17 03:25:06,014] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:06,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:06,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:06,014] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:06,014] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:25:06,015] [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 03:25:06,015] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20548/tc_result.tsv
[2023-03-17 03:25:06,015] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:06,015] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:06,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference/checkm_data
[2023-03-17 03:25:06,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:06,022] [INFO] Task started: CheckM
[2023-03-17 03:25:06,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20548/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20548/checkm_input OceanDNA-b20548/checkm_result
[2023-03-17 03:25:26,143] [INFO] Task succeeded: CheckM
[2023-03-17 03:25:26,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:25:26,154] [INFO] ===== Completeness check finished =====
[2023-03-17 03:25:26,154] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:25:26,154] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20548/markers.fasta)
[2023-03-17 03:25:26,156] [INFO] Task started: Blastn
[2023-03-17 03:25:26,156] [INFO] Running command: blastn -query OceanDNA-b20548/markers.fasta -db /var/lib/cwl/stg8c65931c-4231-4e29-a490-5d615925efff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20548/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:27,041] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:27,044] [INFO] Selected 9 target genomes.
[2023-03-17 03:25:27,044] [INFO] Target genome list was writen to OceanDNA-b20548/target_genomes_gtdb.txt
[2023-03-17 03:25:27,079] [INFO] Task started: fastANI
[2023-03-17 03:25:27,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e9d0618-48be-4001-9612-4538413f02b7/OceanDNA-b20548.fa --refList OceanDNA-b20548/target_genomes_gtdb.txt --output OceanDNA-b20548/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:25:29,903] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:29,907] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:25:29,907] [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_002705605.1	s__GCA-002707645 sp002705605	98.0499	350	385	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002707645.1	s__GCA-002707645 sp002707645	81.2191	218	385	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704685.1	s__GCA-002707645 sp002704685	80.3676	266	385	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693365.1	s__GCA-002707645 sp002693365	80.0288	233	385	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
GCA_002717625.1	s__GCA-2717625 sp002717625	76.5515	68	385	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:25:29,908] [INFO] GTDB search result was written to OceanDNA-b20548/result_gtdb.tsv
[2023-03-17 03:25:29,910] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:25:29,913] [INFO] DFAST_QC result json was written to OceanDNA-b20548/dqc_result.json
[2023-03-17 03:25:29,913] [INFO] DFAST_QC completed!
[2023-03-17 03:25:29,913] [INFO] Total running time: 0h0m39s