[2023-03-15 05:29:10,768] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,768] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference
[2023-03-15 05:29:12,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,387] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,387] [INFO] Running command: cat /var/lib/cwl/stg5036f1f2-f5ab-4dd9-ad25-6d2ff531894c/OceanDNA-b25587.fa | prodigal -d OceanDNA-b25587/cds.fna -a OceanDNA-b25587/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:17,740] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:17,740] [INFO] Task started: HMMsearch
[2023-03-15 05:29:17,740] [INFO] Running command: hmmsearch --tblout OceanDNA-b25587/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference/reference_markers.hmm OceanDNA-b25587/protein.faa > /dev/null
[2023-03-15 05:29:17,942] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:17,943] [INFO] Found 6/6 markers.
[2023-03-15 05:29:17,950] [INFO] Query marker FASTA was written to OceanDNA-b25587/markers.fasta
[2023-03-15 05:29:17,951] [INFO] Task started: Blastn
[2023-03-15 05:29:17,951] [INFO] Running command: blastn -query OceanDNA-b25587/markers.fasta -db /var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference/reference_markers.fasta -out OceanDNA-b25587/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:19,382] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:19,382] [INFO] Selected 19 target genomes.
[2023-03-15 05:29:19,383] [INFO] Target genome list was writen to OceanDNA-b25587/target_genomes.txt
[2023-03-15 05:29:19,400] [INFO] Task started: fastANI
[2023-03-15 05:29:19,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg5036f1f2-f5ab-4dd9-ad25-6d2ff531894c/OceanDNA-b25587.fa --refList OceanDNA-b25587/target_genomes.txt --output OceanDNA-b25587/fastani_result.tsv --threads 1
[2023-03-15 05:29:28,945] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:28,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:28,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:28,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:28,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:29:28,946] [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
--------------------------------------------------------------------------------
[2023-03-15 05:29:28,946] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25587/tc_result.tsv
[2023-03-15 05:29:28,946] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:28,946] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:28,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference/checkm_data
[2023-03-15 05:29:28,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:28,951] [INFO] Task started: CheckM
[2023-03-15 05:29:28,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25587/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25587/checkm_input OceanDNA-b25587/checkm_result
[2023-03-15 05:29:49,200] [INFO] Task succeeded: CheckM
[2023-03-15 05:29:49,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 05:29:49,202] [INFO] ===== Completeness check finished =====
[2023-03-15 05:29:49,202] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:29:49,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25587/markers.fasta)
[2023-03-15 05:29:49,202] [INFO] Task started: Blastn
[2023-03-15 05:29:49,202] [INFO] Running command: blastn -query OceanDNA-b25587/markers.fasta -db /var/lib/cwl/stg80432b6b-7c9f-4faf-9b5b-f51d8241ec6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25587/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:50,322] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:50,323] [INFO] Selected 15 target genomes.
[2023-03-15 05:29:50,323] [INFO] Target genome list was writen to OceanDNA-b25587/target_genomes_gtdb.txt
[2023-03-15 05:29:50,338] [INFO] Task started: fastANI
[2023-03-15 05:29:50,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg5036f1f2-f5ab-4dd9-ad25-6d2ff531894c/OceanDNA-b25587.fa --refList OceanDNA-b25587/target_genomes_gtdb.txt --output OceanDNA-b25587/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:29:53,726] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:53,731] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:29:53,731] [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_008638225.1	s__IMCC9063 sp008638225	96.9036	249	271	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.77	99.77	0.92	0.92	2	conclusive
GCA_018402735.1	s__IMCC9063 sp000750175	94.2531	253	271	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.21	99.21	0.97	0.97	2	-
GCA_008638205.1	s__IMCC9063 sp008638205	78.4641	128	271	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	97.30	96.70	0.84	0.65	4	-
GCA_008638015.1	s__IMCC9063 sp008638015	78.4578	136	271	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.18	98.68	0.91	0.88	9	-
GCA_008638025.1	s__IMCC9063 sp008638025	78.2565	112	271	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195085.1	s__IMCC9063 sp000195085	78.1855	140	271	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:29:53,732] [INFO] GTDB search result was written to OceanDNA-b25587/result_gtdb.tsv
[2023-03-15 05:29:53,732] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:29:53,732] [INFO] DFAST_QC result json was written to OceanDNA-b25587/dqc_result.json
[2023-03-15 05:29:53,732] [INFO] DFAST_QC completed!
[2023-03-15 05:29:53,733] [INFO] Total running time: 0h0m43s