[2023-03-18 00:53:42,860] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,860] [INFO] DQC Reference Directory: /var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference
[2023-03-18 00:53:44,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,409] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,409] [INFO] Running command: cat /var/lib/cwl/stgdb02fce2-e24c-46a1-9de4-d215cd6b8ad4/OceanDNA-b46074.fa | prodigal -d OceanDNA-b46074/cds.fna -a OceanDNA-b46074/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:16,650] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:16,651] [INFO] Task started: HMMsearch
[2023-03-18 00:54:16,651] [INFO] Running command: hmmsearch --tblout OceanDNA-b46074/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference/reference_markers.hmm OceanDNA-b46074/protein.faa > /dev/null
[2023-03-18 00:54:16,845] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:16,846] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb02fce2-e24c-46a1-9de4-d215cd6b8ad4/OceanDNA-b46074.fa]
[2023-03-18 00:54:16,869] [INFO] Query marker FASTA was written to OceanDNA-b46074/markers.fasta
[2023-03-18 00:54:16,870] [INFO] Task started: Blastn
[2023-03-18 00:54:16,870] [INFO] Running command: blastn -query OceanDNA-b46074/markers.fasta -db /var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference/reference_markers.fasta -out OceanDNA-b46074/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:17,440] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:17,441] [INFO] Selected 15 target genomes.
[2023-03-18 00:54:17,441] [INFO] Target genome list was writen to OceanDNA-b46074/target_genomes.txt
[2023-03-18 00:54:17,450] [INFO] Task started: fastANI
[2023-03-18 00:54:17,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb02fce2-e24c-46a1-9de4-d215cd6b8ad4/OceanDNA-b46074.fa --refList OceanDNA-b46074/target_genomes.txt --output OceanDNA-b46074/fastani_result.tsv --threads 1
[2023-03-18 00:54:27,435] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:27,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:27,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:27,440] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:27,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:27,440] [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
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	77.0739	95	1284	95	below_threshold
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.656	118	1284	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:27,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46074/tc_result.tsv
[2023-03-18 00:54:27,440] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:27,440] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:27,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference/checkm_data
[2023-03-18 00:54:27,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:27,446] [INFO] Task started: CheckM
[2023-03-18 00:54:27,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46074/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46074/checkm_input OceanDNA-b46074/checkm_result
[2023-03-18 00:55:46,661] [INFO] Task succeeded: CheckM
[2023-03-18 00:55:46,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:55:46,664] [INFO] ===== Completeness check finished =====
[2023-03-18 00:55:46,664] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:55:46,664] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46074/markers.fasta)
[2023-03-18 00:55:46,665] [INFO] Task started: Blastn
[2023-03-18 00:55:46,665] [INFO] Running command: blastn -query OceanDNA-b46074/markers.fasta -db /var/lib/cwl/stge663b6cb-ac7e-4c62-a111-ad7ccdb02694/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46074/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:55:47,633] [INFO] Task succeeded: Blastn
[2023-03-18 00:55:47,634] [INFO] Selected 15 target genomes.
[2023-03-18 00:55:47,634] [INFO] Target genome list was writen to OceanDNA-b46074/target_genomes_gtdb.txt
[2023-03-18 00:55:47,642] [INFO] Task started: fastANI
[2023-03-18 00:55:47,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb02fce2-e24c-46a1-9de4-d215cd6b8ad4/OceanDNA-b46074.fa --refList OceanDNA-b46074/target_genomes_gtdb.txt --output OceanDNA-b46074/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:55,691] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:55,699] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:55:55,699] [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_002729725.1	s__UBA7441 sp002729725	99.953	1233	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	conclusive
GCA_905182465.1	s__UBA7441 sp905182465	77.9203	151	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480015.1	s__UBA7441 sp002480015	77.8066	188	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	-
GCA_009886465.1	s__UBA7441 sp009886465	77.6646	131	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	97.11	97.11	0.79	0.79	2	-
GCF_902728235.1	s__BACL24 sp902728235	77.6021	181	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
GCA_905479975.1	s__BACL24 sp905479975	77.5263	165	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587165.1	s__UBA7441 sp902587165	77.5111	116	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692545.1	s__UBA7441 sp007692545	77.4322	149	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331195.1	s__UBA7441 sp003331195	77.3896	138	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854655.1	s__BACL24 sp017854655	77.3696	119	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
GCA_018607135.1	s__BACL24 sp003485085	77.3579	138	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
GCA_003503355.1	s__BACL24 sp003503355	76.9797	96	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	98.98	98.98	0.82	0.82	2	-
GCA_018402305.1	s__UBA7441 sp018402305	76.7557	116	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908325.1	s__UBA7441 sp009908325	76.6481	155	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:55:55,700] [INFO] GTDB search result was written to OceanDNA-b46074/result_gtdb.tsv
[2023-03-18 00:55:55,700] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:55,701] [INFO] DFAST_QC result json was written to OceanDNA-b46074/dqc_result.json
[2023-03-18 00:55:55,701] [INFO] DFAST_QC completed!
[2023-03-18 00:55:55,701] [INFO] Total running time: 0h2m13s