[2023-03-14 11:14:12,735] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference
[2023-03-14 11:14:14,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,203] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,203] [INFO] Running command: cat /var/lib/cwl/stg53e7e338-6038-431b-9aaf-8ed24eaaf1c6/OceanDNA-b30912.fa | prodigal -d OceanDNA-b30912/cds.fna -a OceanDNA-b30912/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:44,945] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:44,946] [INFO] Task started: HMMsearch
[2023-03-14 11:14:44,946] [INFO] Running command: hmmsearch --tblout OceanDNA-b30912/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference/reference_markers.hmm OceanDNA-b30912/protein.faa > /dev/null
[2023-03-14 11:14:45,178] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:45,179] [INFO] Found 6/6 markers.
[2023-03-14 11:14:45,208] [INFO] Query marker FASTA was written to OceanDNA-b30912/markers.fasta
[2023-03-14 11:14:45,208] [INFO] Task started: Blastn
[2023-03-14 11:14:45,208] [INFO] Running command: blastn -query OceanDNA-b30912/markers.fasta -db /var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference/reference_markers.fasta -out OceanDNA-b30912/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:45,880] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:45,881] [INFO] Selected 11 target genomes.
[2023-03-14 11:14:45,881] [INFO] Target genome list was writen to OceanDNA-b30912/target_genomes.txt
[2023-03-14 11:14:45,890] [INFO] Task started: fastANI
[2023-03-14 11:14:45,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg53e7e338-6038-431b-9aaf-8ed24eaaf1c6/OceanDNA-b30912.fa --refList OceanDNA-b30912/target_genomes.txt --output OceanDNA-b30912/fastani_result.tsv --threads 1
[2023-03-14 11:14:55,430] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:55,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:55,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:55,436] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:55,436] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:55,436] [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
Thalassospira xianhensis	strain=MCCC 1A02616	GCA_003326475.1	478503	478503	type	True	94.3326	1332	1549	95	below_threshold
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	90.9757	1304	1549	95	below_threshold
Thalassospira xiamenensis	strain=M-5	GCA_000300235.2	220697	220697	suspected-type	True	90.9421	1315	1549	95	below_threshold
Thalassospira permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	90.882	1272	1549	95	below_threshold
Thalassospira alkalitolerans	strain=JCM 18968	GCA_002115745.1	1293890	1293890	type	True	83.2162	1156	1549	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	81.3842	888	1549	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:55,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30912/tc_result.tsv
[2023-03-14 11:14:55,436] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:55,436] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:55,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference/checkm_data
[2023-03-14 11:14:55,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:55,461] [INFO] Task started: CheckM
[2023-03-14 11:14:55,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30912/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30912/checkm_input OceanDNA-b30912/checkm_result
[2023-03-14 11:16:10,437] [INFO] Task succeeded: CheckM
[2023-03-14 11:16:10,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:16:10,440] [INFO] ===== Completeness check finished =====
[2023-03-14 11:16:10,440] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:16:10,440] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30912/markers.fasta)
[2023-03-14 11:16:10,442] [INFO] Task started: Blastn
[2023-03-14 11:16:10,442] [INFO] Running command: blastn -query OceanDNA-b30912/markers.fasta -db /var/lib/cwl/stg20a99573-3127-4322-ae07-e17cf06644ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30912/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:16:11,613] [INFO] Task succeeded: Blastn
[2023-03-14 11:16:11,614] [INFO] Selected 7 target genomes.
[2023-03-14 11:16:11,614] [INFO] Target genome list was writen to OceanDNA-b30912/target_genomes_gtdb.txt
[2023-03-14 11:16:11,621] [INFO] Task started: fastANI
[2023-03-14 11:16:11,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg53e7e338-6038-431b-9aaf-8ed24eaaf1c6/OceanDNA-b30912.fa --refList OceanDNA-b30912/target_genomes_gtdb.txt --output OceanDNA-b30912/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:16:19,471] [INFO] Task succeeded: fastANI
[2023-03-14 11:16:19,476] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:16:19,477] [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_001613805.1	s__Thalassospira lucentensis_A	98.7315	1469	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.23	97.17	0.91	0.86	8	conclusive
GCF_003326475.1	s__Thalassospira xianhensis	94.3326	1332	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115785.1	s__Thalassospira sp002115785	92.3594	1295	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300235.2	s__Thalassospira xiamenensis	90.9421	1315	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.55	97.14	0.89	0.82	23	-
GCF_002115745.1	s__Thalassospira alkalitolerans	83.2162	1156	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326675.1	s__Thalassospira profundimaris_D	81.4684	949	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326795.1	s__Thalassospira profundimaris_C	81.333	920	1549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:16:19,477] [INFO] GTDB search result was written to OceanDNA-b30912/result_gtdb.tsv
[2023-03-14 11:16:19,477] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:16:19,478] [INFO] DFAST_QC result json was written to OceanDNA-b30912/dqc_result.json
[2023-03-14 11:16:19,478] [INFO] DFAST_QC completed!
[2023-03-14 11:16:19,478] [INFO] Total running time: 0h2m7s