[2023-03-16 21:45:15,221] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,222] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference
[2023-03-16 21:45:16,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,378] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,378] [INFO] Running command: cat /var/lib/cwl/stgd9a29184-b9b5-4731-ad69-2c75c95ab3da/OceanDNA-b17766.fa | prodigal -d OceanDNA-b17766/cds.fna -a OceanDNA-b17766/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:50,315] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:50,315] [INFO] Task started: HMMsearch
[2023-03-16 21:45:50,315] [INFO] Running command: hmmsearch --tblout OceanDNA-b17766/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference/reference_markers.hmm OceanDNA-b17766/protein.faa > /dev/null
[2023-03-16 21:45:50,614] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:50,615] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9a29184-b9b5-4731-ad69-2c75c95ab3da/OceanDNA-b17766.fa]
[2023-03-16 21:45:50,651] [INFO] Query marker FASTA was written to OceanDNA-b17766/markers.fasta
[2023-03-16 21:45:50,651] [INFO] Task started: Blastn
[2023-03-16 21:45:50,651] [INFO] Running command: blastn -query OceanDNA-b17766/markers.fasta -db /var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference/reference_markers.fasta -out OceanDNA-b17766/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:51,190] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:51,191] [INFO] Selected 30 target genomes.
[2023-03-16 21:45:51,191] [INFO] Target genome list was writen to OceanDNA-b17766/target_genomes.txt
[2023-03-16 21:45:51,209] [INFO] Task started: fastANI
[2023-03-16 21:45:51,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a29184-b9b5-4731-ad69-2c75c95ab3da/OceanDNA-b17766.fa --refList OceanDNA-b17766/target_genomes.txt --output OceanDNA-b17766/fastani_result.tsv --threads 1
[2023-03-16 21:46:14,048] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:14,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:46:14,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:46:14,057] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:46:14,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:46:14,057] [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
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.7533	82	1818	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.7485	83	1818	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.7147	57	1818	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.6935	50	1818	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	74.6706	72	1818	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	74.6549	59	1818	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	74.6477	61	1818	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	74.6378	66	1818	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.6284	69	1818	95	below_threshold
Streptomyces bambusae	strain=T110	GCA_020532645.1	1550616	1550616	type	True	74.5453	69	1818	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	74.5262	77	1818	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	74.5246	60	1818	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:46:14,057] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17766/tc_result.tsv
[2023-03-16 21:46:14,057] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:46:14,057] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:46:14,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference/checkm_data
[2023-03-16 21:46:14,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:46:14,065] [INFO] Task started: CheckM
[2023-03-16 21:46:14,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17766/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17766/checkm_input OceanDNA-b17766/checkm_result
[2023-03-16 21:47:37,231] [INFO] Task succeeded: CheckM
[2023-03-16 21:47:37,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:47:37,235] [INFO] ===== Completeness check finished =====
[2023-03-16 21:47:37,235] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:47:37,235] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17766/markers.fasta)
[2023-03-16 21:47:37,237] [INFO] Task started: Blastn
[2023-03-16 21:47:37,237] [INFO] Running command: blastn -query OceanDNA-b17766/markers.fasta -db /var/lib/cwl/stg7a83cced-5143-423b-8ae8-e1508f176ef0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17766/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:47:37,996] [INFO] Task succeeded: Blastn
[2023-03-16 21:47:37,996] [INFO] Selected 19 target genomes.
[2023-03-16 21:47:37,997] [INFO] Target genome list was writen to OceanDNA-b17766/target_genomes_gtdb.txt
[2023-03-16 21:47:38,149] [INFO] Task started: fastANI
[2023-03-16 21:47:38,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a29184-b9b5-4731-ad69-2c75c95ab3da/OceanDNA-b17766.fa --refList OceanDNA-b17766/target_genomes_gtdb.txt --output OceanDNA-b17766/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:47:54,242] [INFO] Task succeeded: fastANI
[2023-03-16 21:47:54,250] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:47:54,250] [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_002726335.1	s__UBA8231 sp002726335	99.9217	1605	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018660835.1	s__UBA12574 sp018660835	76.3442	177	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	99.93	99.91	0.98	0.97	7	-
GCA_002725915.1	s__GCA-2725915 sp002725915	76.2052	116	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673255.1	s__UBA12574 sp018673255	76.142	282	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712305.1	s__UBA12574 sp002712305	76.076	164	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	-
GCA_016187725.1	s__SICG01 sp016187725	75.66	163	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867395.1	s__SICG01 sp016867395	75.6287	172	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840005.1	s__GCA-2724215 sp009840005	75.5183	81	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_018672475.1	s__GCA-2724215 sp018672475	75.2943	70	1818	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
GCF_900177295.1	s__Tistlia consotensis	74.7467	84	1818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002344285.1	s__UBA2376 sp002344285	74.6736	84	1818	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000601485.1	s__Chondromyces apiculatus	74.5501	78	1818	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Chondromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:47:54,250] [INFO] GTDB search result was written to OceanDNA-b17766/result_gtdb.tsv
[2023-03-16 21:47:54,250] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:47:54,252] [INFO] DFAST_QC result json was written to OceanDNA-b17766/dqc_result.json
[2023-03-16 21:47:54,252] [INFO] DFAST_QC completed!
[2023-03-16 21:47:54,252] [INFO] Total running time: 0h2m39s