[2023-03-18 02:02:52,818] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:02:52,818] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:02:52,819] [INFO] DQC Reference Directory: /var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference
[2023-03-18 02:02:53,892] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:02:53,893] [INFO] Task started: Prodigal
[2023-03-18 02:02:53,893] [INFO] Running command: cat /var/lib/cwl/stgd77fbfeb-7db1-4b9f-87d8-bf344d59b5c2/OceanDNA-b38423.fa | prodigal -d OceanDNA-b38423/cds.fna -a OceanDNA-b38423/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:03:02,524] [INFO] Task succeeded: Prodigal
[2023-03-18 02:03:02,525] [INFO] Task started: HMMsearch
[2023-03-18 02:03:02,525] [INFO] Running command: hmmsearch --tblout OceanDNA-b38423/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference/reference_markers.hmm OceanDNA-b38423/protein.faa > /dev/null
[2023-03-18 02:03:02,692] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:03:02,693] [INFO] Found 6/6 markers.
[2023-03-18 02:03:02,707] [INFO] Query marker FASTA was written to OceanDNA-b38423/markers.fasta
[2023-03-18 02:03:02,708] [INFO] Task started: Blastn
[2023-03-18 02:03:02,708] [INFO] Running command: blastn -query OceanDNA-b38423/markers.fasta -db /var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference/reference_markers.fasta -out OceanDNA-b38423/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:03:03,282] [INFO] Task succeeded: Blastn
[2023-03-18 02:03:03,283] [INFO] Selected 28 target genomes.
[2023-03-18 02:03:03,283] [INFO] Target genome list was writen to OceanDNA-b38423/target_genomes.txt
[2023-03-18 02:03:03,334] [INFO] Task started: fastANI
[2023-03-18 02:03:03,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgd77fbfeb-7db1-4b9f-87d8-bf344d59b5c2/OceanDNA-b38423.fa --refList OceanDNA-b38423/target_genomes.txt --output OceanDNA-b38423/fastani_result.tsv --threads 1
[2023-03-18 02:03:20,859] [INFO] Task succeeded: fastANI
[2023-03-18 02:03:20,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:03:20,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:03:20,860] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:03:20,860] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:03:20,860] [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 02:03:20,861] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38423/tc_result.tsv
[2023-03-18 02:03:20,861] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:03:20,861] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:03:20,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference/checkm_data
[2023-03-18 02:03:20,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:03:20,867] [INFO] Task started: CheckM
[2023-03-18 02:03:20,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38423/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38423/checkm_input OceanDNA-b38423/checkm_result
[2023-03-18 02:03:47,716] [INFO] Task succeeded: CheckM
[2023-03-18 02:03:47,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:03:47,719] [INFO] ===== Completeness check finished =====
[2023-03-18 02:03:47,719] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:03:47,719] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38423/markers.fasta)
[2023-03-18 02:03:47,720] [INFO] Task started: Blastn
[2023-03-18 02:03:47,720] [INFO] Running command: blastn -query OceanDNA-b38423/markers.fasta -db /var/lib/cwl/stgad798250-bbe2-42b3-a1ec-edcc3f75b727/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38423/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:03:48,672] [INFO] Task succeeded: Blastn
[2023-03-18 02:03:48,674] [INFO] Selected 8 target genomes.
[2023-03-18 02:03:48,674] [INFO] Target genome list was writen to OceanDNA-b38423/target_genomes_gtdb.txt
[2023-03-18 02:03:48,682] [INFO] Task started: fastANI
[2023-03-18 02:03:48,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgd77fbfeb-7db1-4b9f-87d8-bf344d59b5c2/OceanDNA-b38423.fa --refList OceanDNA-b38423/target_genomes_gtdb.txt --output OceanDNA-b38423/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:03:51,310] [INFO] Task succeeded: fastANI
[2023-03-18 02:03:51,315] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:03:51,316] [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_902558075.1	s__HIMB30 sp902558075	93.1751	312	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541775.1	s__HIMB30 sp902541775	90.8634	252	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536515.1	s__HIMB30 sp902536515	90.0364	218	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705325.1	s__HIMB30 sp002705325	88.8763	376	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.62	96.19	0.76	0.70	4	-
GCA_902594275.1	s__HIMB30 sp902594275	88.0158	237	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227525.2	s__HIMB30 sp000227525	87.5125	394	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.38	98.38	0.91	0.91	2	-
GCA_010024125.1	s__HIMB30 sp010024125	79.6021	194	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.50	98.43	0.79	0.78	4	-
GCA_008087055.1	s__HIMB30 sp008087055	79.1343	208	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:03:51,316] [INFO] GTDB search result was written to OceanDNA-b38423/result_gtdb.tsv
[2023-03-18 02:03:51,316] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:03:51,317] [INFO] DFAST_QC result json was written to OceanDNA-b38423/dqc_result.json
[2023-03-18 02:03:51,317] [INFO] DFAST_QC completed!
[2023-03-18 02:03:51,317] [INFO] Total running time: 0h0m58s