[2023-03-17 15:54:38,130] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:54:38,130] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:54:38,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference
[2023-03-17 15:54:39,417] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:54:39,417] [INFO] Task started: Prodigal
[2023-03-17 15:54:39,417] [INFO] Running command: cat /var/lib/cwl/stgaf0c4f53-7ef6-4192-abf7-adc1ae80891c/OceanDNA-b35243.fa | prodigal -d OceanDNA-b35243/cds.fna -a OceanDNA-b35243/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:54:59,905] [INFO] Task succeeded: Prodigal
[2023-03-17 15:54:59,906] [INFO] Task started: HMMsearch
[2023-03-17 15:54:59,906] [INFO] Running command: hmmsearch --tblout OceanDNA-b35243/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference/reference_markers.hmm OceanDNA-b35243/protein.faa > /dev/null
[2023-03-17 15:55:00,125] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:55:00,126] [INFO] Found 6/6 markers.
[2023-03-17 15:55:00,153] [INFO] Query marker FASTA was written to OceanDNA-b35243/markers.fasta
[2023-03-17 15:55:00,153] [INFO] Task started: Blastn
[2023-03-17 15:55:00,153] [INFO] Running command: blastn -query OceanDNA-b35243/markers.fasta -db /var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference/reference_markers.fasta -out OceanDNA-b35243/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:55:00,768] [INFO] Task succeeded: Blastn
[2023-03-17 15:55:00,769] [INFO] Selected 13 target genomes.
[2023-03-17 15:55:00,769] [INFO] Target genome list was writen to OceanDNA-b35243/target_genomes.txt
[2023-03-17 15:55:00,824] [INFO] Task started: fastANI
[2023-03-17 15:55:00,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf0c4f53-7ef6-4192-abf7-adc1ae80891c/OceanDNA-b35243.fa --refList OceanDNA-b35243/target_genomes.txt --output OceanDNA-b35243/fastani_result.tsv --threads 1
[2023-03-17 15:55:13,423] [INFO] Task succeeded: fastANI
[2023-03-17 15:55:13,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:55:13,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:55:13,429] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:55:13,430] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 15:55:13,430] [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
Shewanella benthica	strain=DSM 8812	GCA_015069875.1	43661	43661	type	True	90.5959	688	1186	95	below_threshold
Shewanella psychropiezotolerans	strain=YLB-06	GCA_007197555.1	2593655	2593655	type	True	89.2681	941	1186	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	85.3388	859	1186	95	below_threshold
Shewanella psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	84.7034	913	1186	95	below_threshold
Shewanella eurypsychrophilus	strain=YLB-08	GCA_007004545.3	2593656	2593656	type	True	80.3473	605	1186	95	below_threshold
Shewanella atlantica	strain=HAW-EB5	GCA_003966265.1	271099	271099	type	True	78.7024	377	1186	95	below_threshold
Shewanella canadensis	strain=HAW-EB2	GCA_003966225.1	271096	271096	type	True	78.5491	372	1186	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.2343	305	1186	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	76.4933	78	1186	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 15:55:13,430] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35243/tc_result.tsv
[2023-03-17 15:55:13,430] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:55:13,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:55:13,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference/checkm_data
[2023-03-17 15:55:13,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:55:13,436] [INFO] Task started: CheckM
[2023-03-17 15:55:13,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35243/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35243/checkm_input OceanDNA-b35243/checkm_result
[2023-03-17 15:56:05,424] [INFO] Task succeeded: CheckM
[2023-03-17 15:56:05,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 15:56:05,427] [INFO] ===== Completeness check finished =====
[2023-03-17 15:56:05,427] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:56:05,428] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35243/markers.fasta)
[2023-03-17 15:56:05,428] [INFO] Task started: Blastn
[2023-03-17 15:56:05,428] [INFO] Running command: blastn -query OceanDNA-b35243/markers.fasta -db /var/lib/cwl/stg5899c347-24da-4cb9-9935-887d505700e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35243/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:56:06,369] [INFO] Task succeeded: Blastn
[2023-03-17 15:56:06,370] [INFO] Selected 7 target genomes.
[2023-03-17 15:56:06,370] [INFO] Target genome list was writen to OceanDNA-b35243/target_genomes_gtdb.txt
[2023-03-17 15:56:06,474] [INFO] Task started: fastANI
[2023-03-17 15:56:06,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf0c4f53-7ef6-4192-abf7-adc1ae80891c/OceanDNA-b35243.fa --refList OceanDNA-b35243/target_genomes_gtdb.txt --output OceanDNA-b35243/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:56:14,547] [INFO] Task succeeded: fastANI
[2023-03-17 15:56:14,552] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 15:56:14,552] [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_013214165.1	s__Shewanella sp013214165	99.7413	1088	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015069875.1	s__Shewanella benthica	90.5618	690	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	-
GCF_000172075.1	s__Shewanella benthica_A	89.6702	863	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.25	96.25	0.86	0.86	2	-
GCF_007197555.1	s__Shewanella sp007197555	89.2741	940	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.43	99.43	0.94	0.94	2	-
GCF_000091325.1	s__Shewanella violacea	85.3113	862	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005305.1	s__Shewanella psychrophila	84.7383	909	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004545.2	s__Shewanella sp007004545	80.3936	602	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-17 15:56:14,552] [INFO] GTDB search result was written to OceanDNA-b35243/result_gtdb.tsv
[2023-03-17 15:56:14,552] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:56:14,553] [INFO] DFAST_QC result json was written to OceanDNA-b35243/dqc_result.json
[2023-03-17 15:56:14,554] [INFO] DFAST_QC completed!
[2023-03-17 15:56:14,554] [INFO] Total running time: 0h1m36s