[2023-03-15 10:09:49,678] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference
[2023-03-15 10:09:51,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stge8eaf7d3-0f78-4273-a4cb-71192e001ffa/OceanDNA-b11839.fa | prodigal -d OceanDNA-b11839/cds.fna -a OceanDNA-b11839/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:08,720] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:08,721] [INFO] Task started: HMMsearch
[2023-03-15 10:10:08,721] [INFO] Running command: hmmsearch --tblout OceanDNA-b11839/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference/reference_markers.hmm OceanDNA-b11839/protein.faa > /dev/null
[2023-03-15 10:10:08,877] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:08,877] [INFO] Found 6/6 markers.
[2023-03-15 10:10:08,891] [INFO] Query marker FASTA was written to OceanDNA-b11839/markers.fasta
[2023-03-15 10:10:08,893] [INFO] Task started: Blastn
[2023-03-15 10:10:08,893] [INFO] Running command: blastn -query OceanDNA-b11839/markers.fasta -db /var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference/reference_markers.fasta -out OceanDNA-b11839/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:09,477] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:09,478] [INFO] Selected 23 target genomes.
[2023-03-15 10:10:09,478] [INFO] Target genome list was writen to OceanDNA-b11839/target_genomes.txt
[2023-03-15 10:10:09,526] [INFO] Task started: fastANI
[2023-03-15 10:10:09,526] [INFO] Running command: fastANI --query /var/lib/cwl/stge8eaf7d3-0f78-4273-a4cb-71192e001ffa/OceanDNA-b11839.fa --refList OceanDNA-b11839/target_genomes.txt --output OceanDNA-b11839/fastani_result.tsv --threads 1
[2023-03-15 10:10:24,327] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:24,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:24,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:24,328] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:24,328] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:10:24,328] [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 10:10:24,328] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11839/tc_result.tsv
[2023-03-15 10:10:24,328] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:24,329] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:24,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference/checkm_data
[2023-03-15 10:10:24,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:24,392] [INFO] Task started: CheckM
[2023-03-15 10:10:24,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11839/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11839/checkm_input OceanDNA-b11839/checkm_result
[2023-03-15 10:11:12,324] [INFO] Task succeeded: CheckM
[2023-03-15 10:11:12,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:11:12,504] [INFO] ===== Completeness check finished =====
[2023-03-15 10:11:12,504] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:11:12,504] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11839/markers.fasta)
[2023-03-15 10:11:12,505] [INFO] Task started: Blastn
[2023-03-15 10:11:12,505] [INFO] Running command: blastn -query OceanDNA-b11839/markers.fasta -db /var/lib/cwl/stg8faa5be5-82fe-4ad4-bebe-7e420788b64c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11839/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:11:13,476] [INFO] Task succeeded: Blastn
[2023-03-15 10:11:13,483] [INFO] Selected 27 target genomes.
[2023-03-15 10:11:13,483] [INFO] Target genome list was writen to OceanDNA-b11839/target_genomes_gtdb.txt
[2023-03-15 10:11:14,299] [INFO] Task started: fastANI
[2023-03-15 10:11:14,299] [INFO] Running command: fastANI --query /var/lib/cwl/stge8eaf7d3-0f78-4273-a4cb-71192e001ffa/OceanDNA-b11839.fa --refList OceanDNA-b11839/target_genomes_gtdb.txt --output OceanDNA-b11839/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:11:26,365] [INFO] Task succeeded: fastANI
[2023-03-15 10:11:26,370] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:11:26,370] [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_002683345.1	s__UBA11663 sp002683345	79.8364	143	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863145.1	s__UBA11663 sp002863145	79.4584	153	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
GCA_011524845.1	s__UBA11663 sp011524845	78.2843	139	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469765.1	s__UBA11663 sp002469765	77.5211	88	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729115.1	s__UBA11663 sp002729115	77.4628	99	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	-
GCA_002313415.1	s__UBA11663 sp002313415	77.2038	73	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	99.13	99.10	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-15 10:11:26,404] [INFO] GTDB search result was written to OceanDNA-b11839/result_gtdb.tsv
[2023-03-15 10:11:26,470] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:11:26,508] [INFO] DFAST_QC result json was written to OceanDNA-b11839/dqc_result.json
[2023-03-15 10:11:26,508] [INFO] DFAST_QC completed!
[2023-03-15 10:11:26,508] [INFO] Total running time: 0h1m37s