[2023-03-18 09:58:36,588] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,588] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference
[2023-03-18 09:58:38,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,401] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,401] [INFO] Running command: cat /var/lib/cwl/stgfbed1d9d-827d-4a14-9448-f22a9b52eaaf/OceanDNA-b45104.fa | prodigal -d OceanDNA-b45104/cds.fna -a OceanDNA-b45104/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:47,225] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:47,225] [INFO] Task started: HMMsearch
[2023-03-18 09:58:47,225] [INFO] Running command: hmmsearch --tblout OceanDNA-b45104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference/reference_markers.hmm OceanDNA-b45104/protein.faa > /dev/null
[2023-03-18 09:58:47,412] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:58:47,413] [INFO] Found 6/6 markers.
[2023-03-18 09:58:47,433] [INFO] Query marker FASTA was written to OceanDNA-b45104/markers.fasta
[2023-03-18 09:58:47,433] [INFO] Task started: Blastn
[2023-03-18 09:58:47,434] [INFO] Running command: blastn -query OceanDNA-b45104/markers.fasta -db /var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference/reference_markers.fasta -out OceanDNA-b45104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:47,945] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:47,946] [INFO] Selected 14 target genomes.
[2023-03-18 09:58:47,946] [INFO] Target genome list was writen to OceanDNA-b45104/target_genomes.txt
[2023-03-18 09:58:47,956] [INFO] Task started: fastANI
[2023-03-18 09:58:47,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbed1d9d-827d-4a14-9448-f22a9b52eaaf/OceanDNA-b45104.fa --refList OceanDNA-b45104/target_genomes.txt --output OceanDNA-b45104/fastani_result.tsv --threads 1
[2023-03-18 09:58:55,637] [INFO] Task succeeded: fastANI
[2023-03-18 09:58:55,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:58:55,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:58:55,637] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:58:55,638] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:58:55,638] [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
--------------------------------------------------------------------------------
[2023-03-18 09:58:55,638] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45104/tc_result.tsv
[2023-03-18 09:58:55,638] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:58:55,638] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:58:55,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference/checkm_data
[2023-03-18 09:58:55,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:58:55,651] [INFO] Task started: CheckM
[2023-03-18 09:58:55,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45104/checkm_input OceanDNA-b45104/checkm_result
[2023-03-18 09:59:23,366] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:23,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.50%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:23,370] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:23,370] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:23,370] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45104/markers.fasta)
[2023-03-18 09:59:23,371] [INFO] Task started: Blastn
[2023-03-18 09:59:23,371] [INFO] Running command: blastn -query OceanDNA-b45104/markers.fasta -db /var/lib/cwl/stg4217ebed-a48c-4916-a6c9-909e1003cd3d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:24,093] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:24,094] [INFO] Selected 9 target genomes.
[2023-03-18 09:59:24,094] [INFO] Target genome list was writen to OceanDNA-b45104/target_genomes_gtdb.txt
[2023-03-18 09:59:24,105] [INFO] Task started: fastANI
[2023-03-18 09:59:24,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbed1d9d-827d-4a14-9448-f22a9b52eaaf/OceanDNA-b45104.fa --refList OceanDNA-b45104/target_genomes_gtdb.txt --output OceanDNA-b45104/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:59:28,655] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:28,660] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:59:28,660] [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_000224765.2	s__JCVI-SCAAA005 sp000224765	98.27	255	312	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	97.34	96.08	0.74	0.72	3	conclusive
GCA_003541985.1	s__JCVI-SCAAA005 sp003541985	94.1009	233	312	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683655.1	s__JCVI-SCAAA005 sp002683655	87.6039	235	312	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	98.22	98.15	0.75	0.71	3	-
GCA_002730365.1	s__JCVI-SCAAA005 sp002730365	87.3427	175	312	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450295.1	s__JCVI-SCAAA005 sp002450295	86.9151	246	312	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	96.73	95.52	0.71	0.67	8	-
GCA_011522845.1	s__JCVI-SCAAA005 sp011522845	86.0994	267	312	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:59:28,660] [INFO] GTDB search result was written to OceanDNA-b45104/result_gtdb.tsv
[2023-03-18 09:59:28,660] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:59:28,661] [INFO] DFAST_QC result json was written to OceanDNA-b45104/dqc_result.json
[2023-03-18 09:59:28,661] [INFO] DFAST_QC completed!
[2023-03-18 09:59:28,661] [INFO] Total running time: 0h0m52s