[2023-03-15 10:09:49,681] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,681] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/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 10:09:51,538] [INFO] Running command: cat /var/lib/cwl/stg92d08b18-833c-423f-ac44-64ba8f07c3b1/OceanDNA-b21179.fa | prodigal -d OceanDNA-b21179/cds.fna -a OceanDNA-b21179/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:01,806] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:01,806] [INFO] Task started: HMMsearch
[2023-03-15 10:10:01,806] [INFO] Running command: hmmsearch --tblout OceanDNA-b21179/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/dqc_reference/reference_markers.hmm OceanDNA-b21179/protein.faa > /dev/null
[2023-03-15 10:10:01,987] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:01,987] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg92d08b18-833c-423f-ac44-64ba8f07c3b1/OceanDNA-b21179.fa]
[2023-03-15 10:10:02,001] [INFO] Query marker FASTA was written to OceanDNA-b21179/markers.fasta
[2023-03-15 10:10:02,002] [INFO] Task started: Blastn
[2023-03-15 10:10:02,002] [INFO] Running command: blastn -query OceanDNA-b21179/markers.fasta -db /var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/dqc_reference/reference_markers.fasta -out OceanDNA-b21179/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:02,523] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:02,524] [INFO] Selected 23 target genomes.
[2023-03-15 10:10:02,525] [INFO] Target genome list was writen to OceanDNA-b21179/target_genomes.txt
[2023-03-15 10:10:02,568] [INFO] Task started: fastANI
[2023-03-15 10:10:02,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg92d08b18-833c-423f-ac44-64ba8f07c3b1/OceanDNA-b21179.fa --refList OceanDNA-b21179/target_genomes.txt --output OceanDNA-b21179/fastani_result.tsv --threads 1
[2023-03-15 10:10:12,903] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:12,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:12,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:12,904] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:12,904] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:10:12,904] [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 10:10:12,904] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21179/tc_result.tsv
[2023-03-15 10:10:12,904] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:12,904] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:12,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/dqc_reference/checkm_data
[2023-03-15 10:10:12,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:12,950] [INFO] Task started: CheckM
[2023-03-15 10:10:12,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21179/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21179/checkm_input OceanDNA-b21179/checkm_result
[2023-03-15 10:10:42,918] [INFO] Task succeeded: CheckM
[2023-03-15 10:10:42,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:10:42,997] [INFO] ===== Completeness check finished =====
[2023-03-15 10:10:42,997] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:10:42,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21179/markers.fasta)
[2023-03-15 10:10:42,997] [INFO] Task started: Blastn
[2023-03-15 10:10:42,997] [INFO] Running command: blastn -query OceanDNA-b21179/markers.fasta -db /var/lib/cwl/stg38eaa1ae-afe8-4377-8593-6c17527d004d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21179/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:43,795] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:43,798] [INFO] Selected 17 target genomes.
[2023-03-15 10:10:43,798] [INFO] Target genome list was writen to OceanDNA-b21179/target_genomes_gtdb.txt
[2023-03-15 10:10:44,335] [INFO] Task started: fastANI
[2023-03-15 10:10:44,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg92d08b18-833c-423f-ac44-64ba8f07c3b1/OceanDNA-b21179.fa --refList OceanDNA-b21179/target_genomes_gtdb.txt --output OceanDNA-b21179/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:10:51,547] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:51,554] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:10:51,554] [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_002705185.1	s__LS-NOB sp002705185	98.9357	479	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014382285.1	s__LS-NOB sp014382285	80.0849	409	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_905612265.1	s__LS-NOB sp905612265	79.1834	141	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001542995.1	s__LS-NOB sp001542995	78.3224	318	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786505.1	s__LS-NOB sp002786505	78.1755	217	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873635.1	s__LS-NOB sp009873635	77.7009	244	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_018653085.1	s__LS-NOB sp018653085	77.2011	228	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_003545625.1	s__LS-NOB sp003545625	77.0484	152	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_018664975.1	s__LS-NOB sp018664975	76.6632	146	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018702695.1	s__LS-NOB sp018702695	76.5453	121	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	-
GCA_012961055.1	s__LS-NOB sp012961055	76.3981	93	640	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:10:51,556] [INFO] GTDB search result was written to OceanDNA-b21179/result_gtdb.tsv
[2023-03-15 10:10:51,560] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:10:51,563] [INFO] DFAST_QC result json was written to OceanDNA-b21179/dqc_result.json
[2023-03-15 10:10:51,563] [INFO] DFAST_QC completed!
[2023-03-15 10:10:51,563] [INFO] Total running time: 0h1m2s