[2023-03-17 02:49:37,508] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference
[2023-03-17 02:49:38,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,760] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,760] [INFO] Running command: cat /var/lib/cwl/stg634e8ed5-5730-46c2-9c85-f96dfff52fe1/OceanDNA-b9292.fa | prodigal -d OceanDNA-b9292/cds.fna -a OceanDNA-b9292/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:53,331] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:53,331] [INFO] Task started: HMMsearch
[2023-03-17 02:49:53,331] [INFO] Running command: hmmsearch --tblout OceanDNA-b9292/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference/reference_markers.hmm OceanDNA-b9292/protein.faa > /dev/null
[2023-03-17 02:49:53,551] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:53,551] [INFO] Found 6/6 markers.
[2023-03-17 02:49:53,566] [INFO] Query marker FASTA was written to OceanDNA-b9292/markers.fasta
[2023-03-17 02:49:53,567] [INFO] Task started: Blastn
[2023-03-17 02:49:53,567] [INFO] Running command: blastn -query OceanDNA-b9292/markers.fasta -db /var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference/reference_markers.fasta -out OceanDNA-b9292/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:54,144] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:54,145] [INFO] Selected 35 target genomes.
[2023-03-17 02:49:54,145] [INFO] Target genome list was writen to OceanDNA-b9292/target_genomes.txt
[2023-03-17 02:49:54,308] [INFO] Task started: fastANI
[2023-03-17 02:49:54,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg634e8ed5-5730-46c2-9c85-f96dfff52fe1/OceanDNA-b9292.fa --refList OceanDNA-b9292/target_genomes.txt --output OceanDNA-b9292/fastani_result.tsv --threads 1
[2023-03-17 02:50:13,959] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:13,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:13,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:13,960] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:50:13,960] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:50:13,960] [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
--------------------------------------------------------------------------------
[2023-03-17 02:50:13,961] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9292/tc_result.tsv
[2023-03-17 02:50:13,962] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:13,962] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:13,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference/checkm_data
[2023-03-17 02:50:13,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:13,969] [INFO] Task started: CheckM
[2023-03-17 02:50:13,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9292/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9292/checkm_input OceanDNA-b9292/checkm_result
[2023-03-17 02:50:53,194] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:53,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:53,279] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:53,279] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:53,279] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9292/markers.fasta)
[2023-03-17 02:50:53,280] [INFO] Task started: Blastn
[2023-03-17 02:50:53,281] [INFO] Running command: blastn -query OceanDNA-b9292/markers.fasta -db /var/lib/cwl/stgad8e69e6-00b6-4be1-81a2-a9aad11ccb08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9292/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:54,042] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:54,077] [INFO] Selected 22 target genomes.
[2023-03-17 02:50:54,077] [INFO] Target genome list was writen to OceanDNA-b9292/target_genomes_gtdb.txt
[2023-03-17 02:50:54,287] [INFO] Task started: fastANI
[2023-03-17 02:50:54,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg634e8ed5-5730-46c2-9c85-f96dfff52fe1/OceanDNA-b9292.fa --refList OceanDNA-b9292/target_genomes_gtdb.txt --output OceanDNA-b9292/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:51:01,054] [INFO] Task succeeded: fastANI
[2023-03-17 02:51:01,065] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:51:01,065] [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_902546725.1	s__MS024-2A sp902546725	78.9573	229	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167945.1	s__MS024-2A sp002167945	78.3075	236	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858055.1	s__MS024-2A sp002384715	77.8426	205	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_002705385.1	s__MS024-2A sp002705385	77.8271	154	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017851655.1	s__MS024-2A sp017851655	77.6299	226	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_011525195.1	s__MS024-2A sp011525195	77.376	151	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	77.328	128	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_902512755.1	s__MS024-2A sp902512755	77.0221	60	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292265.1	s__MS024-2A sp002292265	77.0053	142	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_905181895.1	s__MS024-2A sp905181895	76.9626	63	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	76.9262	147	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852075.1	s__MS024-2A sp017852075	76.837	143	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_905480425.1	s__MS024-2A sp905480425	76.7692	105	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_905182305.1	s__MS024-2A sp905182305	76.7236	112	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699935.1	s__MS024-2A sp018699935	76.6324	98	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	-
GCA_902517245.1	s__MS024-2A sp902517245	76.5768	78	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606525.1	s__MS024-2A sp902606525	76.5116	62	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618245.1	s__MS024-2A sp902618245	76.4724	60	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_002719315.1	s__GCA-2719315 sp002719315	75.8327	50	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:51:01,079] [INFO] GTDB search result was written to OceanDNA-b9292/result_gtdb.tsv
[2023-03-17 02:51:01,099] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:51:01,112] [INFO] DFAST_QC result json was written to OceanDNA-b9292/dqc_result.json
[2023-03-17 02:51:01,113] [INFO] DFAST_QC completed!
[2023-03-17 02:51:01,113] [INFO] Total running time: 0h1m24s