[2023-03-15 14:37:46,930] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:46,930] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:46,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference
[2023-03-15 14:37:48,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:48,674] [INFO] Task started: Prodigal
[2023-03-15 14:37:48,674] [INFO] Running command: cat /var/lib/cwl/stg2771af31-31d5-43ef-825d-23f07131fc6a/OceanDNA-b35266.fa | prodigal -d OceanDNA-b35266/cds.fna -a OceanDNA-b35266/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:14,338] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:14,338] [INFO] Task started: HMMsearch
[2023-03-15 14:38:14,338] [INFO] Running command: hmmsearch --tblout OceanDNA-b35266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference/reference_markers.hmm OceanDNA-b35266/protein.faa > /dev/null
[2023-03-15 14:38:14,568] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:14,569] [INFO] Found 6/6 markers.
[2023-03-15 14:38:14,611] [INFO] Query marker FASTA was written to OceanDNA-b35266/markers.fasta
[2023-03-15 14:38:14,612] [INFO] Task started: Blastn
[2023-03-15 14:38:14,612] [INFO] Running command: blastn -query OceanDNA-b35266/markers.fasta -db /var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference/reference_markers.fasta -out OceanDNA-b35266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:15,302] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:15,303] [INFO] Selected 8 target genomes.
[2023-03-15 14:38:15,303] [INFO] Target genome list was writen to OceanDNA-b35266/target_genomes.txt
[2023-03-15 14:38:15,307] [INFO] Task started: fastANI
[2023-03-15 14:38:15,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg2771af31-31d5-43ef-825d-23f07131fc6a/OceanDNA-b35266.fa --refList OceanDNA-b35266/target_genomes.txt --output OceanDNA-b35266/fastani_result.tsv --threads 1
[2023-03-15 14:38:24,197] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:24,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:24,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:24,204] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:24,204] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:38:24,204] [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 livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	87.5469	1257	1559	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	85.6623	1208	1559	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	85.6259	1196	1559	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	85.6226	1178	1559	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	85.6107	1236	1559	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	85.5875	1234	1559	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	81.7606	976	1559	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	81.1307	862	1559	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:38:24,204] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35266/tc_result.tsv
[2023-03-15 14:38:24,204] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:24,204] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:24,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference/checkm_data
[2023-03-15 14:38:24,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:24,211] [INFO] Task started: CheckM
[2023-03-15 14:38:24,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35266/checkm_input OceanDNA-b35266/checkm_result
[2023-03-15 14:39:27,179] [INFO] Task succeeded: CheckM
[2023-03-15 14:39:27,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:39:27,190] [INFO] ===== Completeness check finished =====
[2023-03-15 14:39:27,191] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:39:27,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35266/markers.fasta)
[2023-03-15 14:39:27,192] [INFO] Task started: Blastn
[2023-03-15 14:39:27,192] [INFO] Running command: blastn -query OceanDNA-b35266/markers.fasta -db /var/lib/cwl/stg12472f1c-d932-4c76-92f9-75f3a60cb063/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:28,228] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:28,229] [INFO] Selected 7 target genomes.
[2023-03-15 14:39:28,229] [INFO] Target genome list was writen to OceanDNA-b35266/target_genomes_gtdb.txt
[2023-03-15 14:39:28,237] [INFO] Task started: fastANI
[2023-03-15 14:39:28,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg2771af31-31d5-43ef-825d-23f07131fc6a/OceanDNA-b35266.fa --refList OceanDNA-b35266/target_genomes_gtdb.txt --output OceanDNA-b35266/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:39:37,089] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:37,093] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:39:37,094] [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
GCF_003797125.1	s__Shewanella frigidimarina	98.1489	1426	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	conclusive
GCF_010092445.1	s__Shewanella sp002836315	93.8232	1383	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_014164505.1	s__Shewanella sp014164505	92.6216	1058	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	87.5583	1255	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	85.6929	1204	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_003797885.1	s__Shewanella vesiculosa	85.6166	1235	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_003855155.1	s__Shewanella sp002836275	85.6126	1199	1559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-15 14:39:37,094] [INFO] GTDB search result was written to OceanDNA-b35266/result_gtdb.tsv
[2023-03-15 14:39:37,094] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:39:37,095] [INFO] DFAST_QC result json was written to OceanDNA-b35266/dqc_result.json
[2023-03-15 14:39:37,095] [INFO] DFAST_QC completed!
[2023-03-15 14:39:37,095] [INFO] Total running time: 0h1m50s