[2023-03-19 23:03:45,044] [INFO] DFAST_QC pipeline started.
[2023-03-19 23:03:45,052] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 23:03:45,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference
[2023-03-19 23:03:46,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 23:03:46,891] [INFO] Task started: Prodigal
[2023-03-19 23:03:46,891] [INFO] Running command: cat /var/lib/cwl/stgb013c750-7408-4d7f-9464-b01140fdac4e/OceanDNA-b24579.fa | prodigal -d OceanDNA-b24579/cds.fna -a OceanDNA-b24579/protein.faa -g 11 -q > /dev/null
[2023-03-19 23:03:50,663] [INFO] Task succeeded: Prodigal
[2023-03-19 23:03:50,663] [INFO] Task started: HMMsearch
[2023-03-19 23:03:50,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b24579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference/reference_markers.hmm OceanDNA-b24579/protein.faa > /dev/null
[2023-03-19 23:03:50,878] [INFO] Task succeeded: HMMsearch
[2023-03-19 23:03:50,878] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb013c750-7408-4d7f-9464-b01140fdac4e/OceanDNA-b24579.fa]
[2023-03-19 23:03:50,887] [INFO] Query marker FASTA was written to OceanDNA-b24579/markers.fasta
[2023-03-19 23:03:50,916] [INFO] Task started: Blastn
[2023-03-19 23:03:50,917] [INFO] Running command: blastn -query OceanDNA-b24579/markers.fasta -db /var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference/reference_markers.fasta -out OceanDNA-b24579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 23:03:52,930] [INFO] Task succeeded: Blastn
[2023-03-19 23:03:52,930] [INFO] Selected 15 target genomes.
[2023-03-19 23:03:52,931] [INFO] Target genome list was writen to OceanDNA-b24579/target_genomes.txt
[2023-03-19 23:03:52,953] [INFO] Task started: fastANI
[2023-03-19 23:03:52,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgb013c750-7408-4d7f-9464-b01140fdac4e/OceanDNA-b24579.fa --refList OceanDNA-b24579/target_genomes.txt --output OceanDNA-b24579/fastani_result.tsv --threads 1
[2023-03-19 23:03:59,502] [INFO] Task succeeded: fastANI
[2023-03-19 23:03:59,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 23:03:59,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 23:03:59,503] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 23:03:59,503] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 23:03:59,503] [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
--------------------------------------------------------------------------------
[2023-03-19 23:03:59,503] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24579/tc_result.tsv
[2023-03-19 23:03:59,503] [INFO] ===== Taxonomy check completed =====
[2023-03-19 23:03:59,503] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 23:03:59,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference/checkm_data
[2023-03-19 23:03:59,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 23:03:59,508] [INFO] Task started: CheckM
[2023-03-19 23:03:59,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24579/checkm_input OceanDNA-b24579/checkm_result
[2023-03-19 23:04:17,096] [INFO] Task succeeded: CheckM
[2023-03-19 23:04:17,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 23:04:17,098] [INFO] ===== Completeness check finished =====
[2023-03-19 23:04:17,099] [INFO] ===== Start GTDB Search =====
[2023-03-19 23:04:17,099] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24579/markers.fasta)
[2023-03-19 23:04:17,101] [INFO] Task started: Blastn
[2023-03-19 23:04:17,101] [INFO] Running command: blastn -query OceanDNA-b24579/markers.fasta -db /var/lib/cwl/stg81d20d77-75ef-4ce5-93b6-79bf5db7b3da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 23:04:18,141] [INFO] Task succeeded: Blastn
[2023-03-19 23:04:18,142] [INFO] Selected 12 target genomes.
[2023-03-19 23:04:18,142] [INFO] Target genome list was writen to OceanDNA-b24579/target_genomes_gtdb.txt
[2023-03-19 23:04:18,400] [INFO] Task started: fastANI
[2023-03-19 23:04:18,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgb013c750-7408-4d7f-9464-b01140fdac4e/OceanDNA-b24579.fa --refList OceanDNA-b24579/target_genomes_gtdb.txt --output OceanDNA-b24579/fastani_result_gtdb.tsv --threads 1
[2023-03-19 23:04:20,310] [INFO] Task succeeded: fastANI
[2023-03-19 23:04:20,314] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-19 23:04:20,314] [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_902521155.1	s__HIMB59 sp902521155	95.8602	107	136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.50	99.50	0.70	0.70	2	inconclusive
GCA_902515765.1	s__HIMB59 sp902515765	95.2778	91	136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902509695.1	s__HIMB59 sp902509695	80.1303	70	136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902617515.1	s__HIMB59 sp902617515	78.4634	55	136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902621205.1	s__HIMB59 sp902621205	78.4598	57	136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.28	98.69	0.88	0.86	4	-
GCA_902530745.1	s__HIMB59 sp902530745	78.2732	60	136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.01	95.70	0.83	0.77	8	-
--------------------------------------------------------------------------------
[2023-03-19 23:04:20,315] [INFO] GTDB search result was written to OceanDNA-b24579/result_gtdb.tsv
[2023-03-19 23:04:20,315] [INFO] ===== GTDB Search completed =====
[2023-03-19 23:04:20,315] [INFO] DFAST_QC result json was written to OceanDNA-b24579/dqc_result.json
[2023-03-19 23:04:20,315] [INFO] DFAST_QC completed!
[2023-03-19 23:04:20,316] [INFO] Total running time: 0h0m35s