[2023-03-18 22:44:57,929] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference
[2023-03-18 22:44:59,054] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,054] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,054] [INFO] Running command: cat /var/lib/cwl/stg6da7e61d-2852-40fa-90fe-84f74276b883/OceanDNA-b30938.fa | prodigal -d OceanDNA-b30938/cds.fna -a OceanDNA-b30938/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:27,729] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:27,729] [INFO] Task started: HMMsearch
[2023-03-18 22:45:27,729] [INFO] Running command: hmmsearch --tblout OceanDNA-b30938/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference/reference_markers.hmm OceanDNA-b30938/protein.faa > /dev/null
[2023-03-18 22:45:27,949] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:27,949] [INFO] Found 6/6 markers.
[2023-03-18 22:45:27,980] [INFO] Query marker FASTA was written to OceanDNA-b30938/markers.fasta
[2023-03-18 22:45:27,981] [INFO] Task started: Blastn
[2023-03-18 22:45:27,981] [INFO] Running command: blastn -query OceanDNA-b30938/markers.fasta -db /var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference/reference_markers.fasta -out OceanDNA-b30938/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:28,728] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:28,732] [INFO] Selected 12 target genomes.
[2023-03-18 22:45:28,732] [INFO] Target genome list was writen to OceanDNA-b30938/target_genomes.txt
[2023-03-18 22:45:28,739] [INFO] Task started: fastANI
[2023-03-18 22:45:28,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg6da7e61d-2852-40fa-90fe-84f74276b883/OceanDNA-b30938.fa --refList OceanDNA-b30938/target_genomes.txt --output OceanDNA-b30938/fastani_result.tsv --threads 1
[2023-03-18 22:45:39,543] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:39,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:39,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:39,550] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2023-03-18 22:45:39,550] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-18 22:45:39,550] [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 permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	97.7199	1272	1494	95	inconclusive
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	97.422	1301	1494	95	inconclusive
Thalassospira xiamenensis	strain=M-5	GCA_000300235.2	220697	220697	suspected-type	True	97.3859	1317	1494	95	inconclusive
Thalassospira xianhensis	strain=MCCC 1A02616	GCA_003326475.1	478503	478503	type	True	90.7925	1205	1494	95	below_threshold
Thalassospira alkalitolerans	strain=JCM 18968	GCA_002115745.1	1293890	1293890	type	True	83.4252	1100	1494	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	81.4766	908	1494	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	80.7011	813	1494	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	75.9662	53	1494	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:45:39,551] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30938/tc_result.tsv
[2023-03-18 22:45:39,553] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:39,553] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:39,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference/checkm_data
[2023-03-18 22:45:39,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:39,619] [INFO] Task started: CheckM
[2023-03-18 22:45:39,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30938/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30938/checkm_input OceanDNA-b30938/checkm_result
[2023-03-18 22:46:50,385] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:50,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:51,089] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:51,089] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:51,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30938/markers.fasta)
[2023-03-18 22:46:51,089] [INFO] Task started: Blastn
[2023-03-18 22:46:51,089] [INFO] Running command: blastn -query OceanDNA-b30938/markers.fasta -db /var/lib/cwl/stg2ebb193c-5e1f-44fd-b174-e7e4dcb0e11c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30938/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:52,419] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:52,424] [INFO] Selected 7 target genomes.
[2023-03-18 22:46:52,424] [INFO] Target genome list was writen to OceanDNA-b30938/target_genomes_gtdb.txt
[2023-03-18 22:46:52,445] [INFO] Task started: fastANI
[2023-03-18 22:46:52,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg6da7e61d-2852-40fa-90fe-84f74276b883/OceanDNA-b30938.fa --refList OceanDNA-b30938/target_genomes_gtdb.txt --output OceanDNA-b30938/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:46:59,902] [INFO] Task succeeded: fastANI
[2023-03-18 22:46:59,907] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 22:46:59,907] [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_000300235.2	s__Thalassospira xiamenensis	97.4147	1315	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.55	97.14	0.89	0.82	23	inconclusive
GCF_002115785.1	s__Thalassospira sp002115785	95.0349	1277	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_001613805.1	s__Thalassospira lucentensis_A	90.8143	1230	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.23	97.17	0.91	0.86	8	-
GCF_003326475.1	s__Thalassospira xianhensis	90.7925	1205	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115745.1	s__Thalassospira alkalitolerans	83.4171	1101	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	81.4841	907	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_001613795.1	s__Thalassospira sp001613795	81.0356	833	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
--------------------------------------------------------------------------------
[2023-03-18 22:46:59,910] [INFO] GTDB search result was written to OceanDNA-b30938/result_gtdb.tsv
[2023-03-18 22:46:59,910] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:46:59,913] [INFO] DFAST_QC result json was written to OceanDNA-b30938/dqc_result.json
[2023-03-18 22:46:59,913] [INFO] DFAST_QC completed!
[2023-03-18 22:46:59,913] [INFO] Total running time: 0h2m2s