[2023-03-19 00:33:18,978] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:18,979] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:18,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference
[2023-03-19 00:33:20,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,220] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,220] [INFO] Running command: cat /var/lib/cwl/stg649911d8-2f1e-440e-8f4b-5b3fc0dcf6ff/OceanDNA-b46695.fa | prodigal -d OceanDNA-b46695/cds.fna -a OceanDNA-b46695/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:41,463] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:41,463] [INFO] Task started: HMMsearch
[2023-03-19 00:33:41,463] [INFO] Running command: hmmsearch --tblout OceanDNA-b46695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference/reference_markers.hmm OceanDNA-b46695/protein.faa > /dev/null
[2023-03-19 00:33:41,689] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:41,690] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg649911d8-2f1e-440e-8f4b-5b3fc0dcf6ff/OceanDNA-b46695.fa]
[2023-03-19 00:33:41,713] [INFO] Query marker FASTA was written to OceanDNA-b46695/markers.fasta
[2023-03-19 00:33:41,715] [INFO] Task started: Blastn
[2023-03-19 00:33:41,715] [INFO] Running command: blastn -query OceanDNA-b46695/markers.fasta -db /var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference/reference_markers.fasta -out OceanDNA-b46695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:42,250] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:42,252] [INFO] Selected 15 target genomes.
[2023-03-19 00:33:42,252] [INFO] Target genome list was writen to OceanDNA-b46695/target_genomes.txt
[2023-03-19 00:33:42,266] [INFO] Task started: fastANI
[2023-03-19 00:33:42,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg649911d8-2f1e-440e-8f4b-5b3fc0dcf6ff/OceanDNA-b46695.fa --refList OceanDNA-b46695/target_genomes.txt --output OceanDNA-b46695/fastani_result.tsv --threads 1
[2023-03-19 00:33:55,398] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:55,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:55,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:55,399] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:55,399] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:33:55,399] [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
--------------------------------------------------------------------------------
[2023-03-19 00:33:55,400] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46695/tc_result.tsv
[2023-03-19 00:33:55,400] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:55,400] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:55,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference/checkm_data
[2023-03-19 00:33:55,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:55,409] [INFO] Task started: CheckM
[2023-03-19 00:33:55,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46695/checkm_input OceanDNA-b46695/checkm_result
[2023-03-19 00:34:51,633] [INFO] Task succeeded: CheckM
[2023-03-19 00:34:51,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.90%
Contamintation: 8.85%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-19 00:34:51,639] [INFO] ===== Completeness check finished =====
[2023-03-19 00:34:51,639] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:34:51,639] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46695/markers.fasta)
[2023-03-19 00:34:51,641] [INFO] Task started: Blastn
[2023-03-19 00:34:51,641] [INFO] Running command: blastn -query OceanDNA-b46695/markers.fasta -db /var/lib/cwl/stg9a40a9d8-47ba-4f5f-bc2d-11b7e832b82b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:52,304] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:52,306] [INFO] Selected 15 target genomes.
[2023-03-19 00:34:52,306] [INFO] Target genome list was writen to OceanDNA-b46695/target_genomes_gtdb.txt
[2023-03-19 00:34:52,314] [INFO] Task started: fastANI
[2023-03-19 00:34:52,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg649911d8-2f1e-440e-8f4b-5b3fc0dcf6ff/OceanDNA-b46695.fa --refList OceanDNA-b46695/target_genomes_gtdb.txt --output OceanDNA-b46695/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:35:00,380] [INFO] Task succeeded: fastANI
[2023-03-19 00:35:00,384] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:35:00,384] [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_002709395.1	s__Roseibacillus_B sp002709395	90.6105	495	615	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.31	97.31	0.76	0.76	2	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	79.3315	248	615	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	79.0144	182	615	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501065.1	s__Roseibacillus_B sp002501065	78.7546	354	615	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_003483645.1	s__Roseibacillus_B sp003483645	78.5222	213	615	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:35:00,386] [INFO] GTDB search result was written to OceanDNA-b46695/result_gtdb.tsv
[2023-03-19 00:35:00,386] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:35:00,388] [INFO] DFAST_QC result json was written to OceanDNA-b46695/dqc_result.json
[2023-03-19 00:35:00,388] [INFO] DFAST_QC completed!
[2023-03-19 00:35:00,388] [INFO] Total running time: 0h1m41s