[2023-03-17 03:19:35,922] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:19:35,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:19:35,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference
[2023-03-17 03:19:37,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:19:37,063] [INFO] Task started: Prodigal
[2023-03-17 03:19:37,063] [INFO] Running command: cat /var/lib/cwl/stg9d88704f-508b-45c1-b5ca-bd8ee73342cf/OceanDNA-b3075.fa | prodigal -d OceanDNA-b3075/cds.fna -a OceanDNA-b3075/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:19:42,736] [INFO] Task succeeded: Prodigal
[2023-03-17 03:19:42,736] [INFO] Task started: HMMsearch
[2023-03-17 03:19:42,736] [INFO] Running command: hmmsearch --tblout OceanDNA-b3075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference/reference_markers.hmm OceanDNA-b3075/protein.faa > /dev/null
[2023-03-17 03:19:42,897] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:19:42,897] [INFO] Found 6/6 markers.
[2023-03-17 03:19:42,906] [INFO] Query marker FASTA was written to OceanDNA-b3075/markers.fasta
[2023-03-17 03:19:42,907] [INFO] Task started: Blastn
[2023-03-17 03:19:42,907] [INFO] Running command: blastn -query OceanDNA-b3075/markers.fasta -db /var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference/reference_markers.fasta -out OceanDNA-b3075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:19:43,653] [INFO] Task succeeded: Blastn
[2023-03-17 03:19:43,654] [INFO] Selected 22 target genomes.
[2023-03-17 03:19:43,654] [INFO] Target genome list was writen to OceanDNA-b3075/target_genomes.txt
[2023-03-17 03:19:43,664] [INFO] Task started: fastANI
[2023-03-17 03:19:43,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d88704f-508b-45c1-b5ca-bd8ee73342cf/OceanDNA-b3075.fa --refList OceanDNA-b3075/target_genomes.txt --output OceanDNA-b3075/fastani_result.tsv --threads 1
[2023-03-17 03:19:55,043] [INFO] Task succeeded: fastANI
[2023-03-17 03:19:55,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:19:55,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:19:55,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:19:55,044] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:19:55,044] [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 03:19:55,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3075/tc_result.tsv
[2023-03-17 03:19:55,044] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:19:55,044] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:19:55,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference/checkm_data
[2023-03-17 03:19:55,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:19:55,050] [INFO] Task started: CheckM
[2023-03-17 03:19:55,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3075/checkm_input OceanDNA-b3075/checkm_result
[2023-03-17 03:20:17,878] [INFO] Task succeeded: CheckM
[2023-03-17 03:20:17,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:20:17,900] [INFO] ===== Completeness check finished =====
[2023-03-17 03:20:17,901] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:20:17,901] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3075/markers.fasta)
[2023-03-17 03:20:17,902] [INFO] Task started: Blastn
[2023-03-17 03:20:17,902] [INFO] Running command: blastn -query OceanDNA-b3075/markers.fasta -db /var/lib/cwl/stgf935e7d4-daf8-4c3c-a27e-1bc0ccf92e97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:20:19,114] [INFO] Task succeeded: Blastn
[2023-03-17 03:20:19,120] [INFO] Selected 18 target genomes.
[2023-03-17 03:20:19,120] [INFO] Target genome list was writen to OceanDNA-b3075/target_genomes_gtdb.txt
[2023-03-17 03:20:19,314] [INFO] Task started: fastANI
[2023-03-17 03:20:19,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d88704f-508b-45c1-b5ca-bd8ee73342cf/OceanDNA-b3075.fa --refList OceanDNA-b3075/target_genomes_gtdb.txt --output OceanDNA-b3075/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:20:23,030] [INFO] Task succeeded: fastANI
[2023-03-17 03:20:23,039] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:20:23,040] [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_000372185.1	s__Planktophila sp000372185	78.7892	90	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288105.1	s__Planktophila versatilis	78.7096	116	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.43	95.84	0.93	0.91	4	-
GCF_002288225.1	s__Planktophila dulcis	78.5631	142	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.64	97.42	0.94	0.93	3	-
GCF_002288065.1	s__Planktophila sulfonica	78.5505	135	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002284855.1	s__Planktophila sp002284855	78.5269	130	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002430075.1	s__Planktophila sp002430075	78.2745	91	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845465.1	s__Planktophila sp903845465	78.1839	106	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.37	98.68	0.87	0.84	5	-
GCA_903865885.1	s__Planktophila sp903865885	77.9083	91	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287925.1	s__Planktophila lacus	77.864	90	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	95.55	95.24	0.96	0.95	3	-
GCF_002288185.1	s__Planktophila vernalis	77.5483	58	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923805.1	s__Planktophila sp009923805	77.5377	110	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701085.1	s__Planktophila sp009701085	77.5306	59	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.29	98.29	0.74	0.74	2	-
GCA_009698845.1	s__Planktophila sp009698845	77.4138	85	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009700365.1	s__Planktophila sp009700365	77.3677	84	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.64	98.64	0.85	0.85	2	-
GCA_010024385.1	s__Planktophila sp010024385	77.3326	54	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.43	99.35	0.91	0.87	13	-
GCA_009705185.1	s__Planktophila sp009705185	77.0187	77	342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:20:23,040] [INFO] GTDB search result was written to OceanDNA-b3075/result_gtdb.tsv
[2023-03-17 03:20:23,040] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:20:23,041] [INFO] DFAST_QC result json was written to OceanDNA-b3075/dqc_result.json
[2023-03-17 03:20:23,041] [INFO] DFAST_QC completed!
[2023-03-17 03:20:23,041] [INFO] Total running time: 0h0m47s