[2023-03-15 09:48:16,568] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,568] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,568] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference
[2023-03-15 09:48:18,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,226] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,227] [INFO] Running command: cat /var/lib/cwl/stgf9dcb967-092e-4bd9-a533-57e2c7a523bc/OceanDNA-b44823.fa | prodigal -d OceanDNA-b44823/cds.fna -a OceanDNA-b44823/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:28,709] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:28,710] [INFO] Task started: HMMsearch
[2023-03-15 09:48:28,710] [INFO] Running command: hmmsearch --tblout OceanDNA-b44823/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference/reference_markers.hmm OceanDNA-b44823/protein.faa > /dev/null
[2023-03-15 09:48:28,875] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:28,876] [INFO] Found 6/6 markers.
[2023-03-15 09:48:28,895] [INFO] Query marker FASTA was written to OceanDNA-b44823/markers.fasta
[2023-03-15 09:48:28,895] [INFO] Task started: Blastn
[2023-03-15 09:48:28,895] [INFO] Running command: blastn -query OceanDNA-b44823/markers.fasta -db /var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference/reference_markers.fasta -out OceanDNA-b44823/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:29,403] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:29,404] [INFO] Selected 8 target genomes.
[2023-03-15 09:48:29,405] [INFO] Target genome list was writen to OceanDNA-b44823/target_genomes.txt
[2023-03-15 09:48:29,409] [INFO] Task started: fastANI
[2023-03-15 09:48:29,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9dcb967-092e-4bd9-a533-57e2c7a523bc/OceanDNA-b44823.fa --refList OceanDNA-b44823/target_genomes.txt --output OceanDNA-b44823/fastani_result.tsv --threads 1
[2023-03-15 09:48:33,292] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:33,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:33,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:33,293] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:33,293] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:33,293] [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 09:48:33,293] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44823/tc_result.tsv
[2023-03-15 09:48:33,293] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:33,293] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:33,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference/checkm_data
[2023-03-15 09:48:33,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:33,301] [INFO] Task started: CheckM
[2023-03-15 09:48:33,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44823/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44823/checkm_input OceanDNA-b44823/checkm_result
[2023-03-15 09:49:05,635] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:05,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:05,637] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:05,637] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:05,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44823/markers.fasta)
[2023-03-15 09:49:05,638] [INFO] Task started: Blastn
[2023-03-15 09:49:05,638] [INFO] Running command: blastn -query OceanDNA-b44823/markers.fasta -db /var/lib/cwl/stgfda21a64-d8a5-4bb0-8a51-7ee73ca79eef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44823/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:06,341] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:06,342] [INFO] Selected 10 target genomes.
[2023-03-15 09:49:06,342] [INFO] Target genome list was writen to OceanDNA-b44823/target_genomes_gtdb.txt
[2023-03-15 09:49:06,651] [INFO] Task started: fastANI
[2023-03-15 09:49:06,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9dcb967-092e-4bd9-a533-57e2c7a523bc/OceanDNA-b44823.fa --refList OceanDNA-b44823/target_genomes_gtdb.txt --output OceanDNA-b44823/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:11,674] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:11,680] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:11,681] [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_002082305.1	s__Arctic96AD-7 sp002082305	80.4534	223	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
GCA_902513935.1	s__Arctic96AD-7 sp902513935	79.7169	110	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182865.1	s__Arctic96AD-7 sp905182865	79.622	211	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.26	97.17	0.94	0.88	7	-
GCA_016764995.1	s__Arctic96AD-7 sp016764995	78.6442	166	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964265.1	s__Arctic96AD-7 sp012964265	78.5269	163	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.25	98.98	0.81	0.73	8	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	78.0113	153	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
GCA_018645085.1	s__Arctic96AD-7 sp018645085	77.808	144	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382365.1	s__Arctic96AD-7 sp014382365	77.4788	139	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.95	99.95	0.98	0.98	2	-
GCA_001627865.1	s__Arctic96AD-7 sp001627865	76.7077	120	295	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.71	99.45	0.95	0.94	9	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:11,681] [INFO] GTDB search result was written to OceanDNA-b44823/result_gtdb.tsv
[2023-03-15 09:49:11,681] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:11,682] [INFO] DFAST_QC result json was written to OceanDNA-b44823/dqc_result.json
[2023-03-15 09:49:11,682] [INFO] DFAST_QC completed!
[2023-03-15 09:49:11,682] [INFO] Total running time: 0h0m55s