[2023-03-19 00:15:41,728] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference
[2023-03-19 00:15:43,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,444] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,444] [INFO] Running command: cat /var/lib/cwl/stgf43ce0ce-cbdf-4c73-9eac-5106b1da1bab/OceanDNA-b17713.fa | prodigal -d OceanDNA-b17713/cds.fna -a OceanDNA-b17713/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:16,832] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:16,832] [INFO] Task started: HMMsearch
[2023-03-19 00:16:16,832] [INFO] Running command: hmmsearch --tblout OceanDNA-b17713/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference/reference_markers.hmm OceanDNA-b17713/protein.faa > /dev/null
[2023-03-19 00:16:17,072] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:17,072] [INFO] Found 6/6 markers.
[2023-03-19 00:16:17,107] [INFO] Query marker FASTA was written to OceanDNA-b17713/markers.fasta
[2023-03-19 00:16:17,107] [INFO] Task started: Blastn
[2023-03-19 00:16:17,108] [INFO] Running command: blastn -query OceanDNA-b17713/markers.fasta -db /var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference/reference_markers.fasta -out OceanDNA-b17713/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:17,643] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:17,644] [INFO] Selected 27 target genomes.
[2023-03-19 00:16:17,644] [INFO] Target genome list was writen to OceanDNA-b17713/target_genomes.txt
[2023-03-19 00:16:17,663] [INFO] Task started: fastANI
[2023-03-19 00:16:17,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgf43ce0ce-cbdf-4c73-9eac-5106b1da1bab/OceanDNA-b17713.fa --refList OceanDNA-b17713/target_genomes.txt --output OceanDNA-b17713/fastani_result.tsv --threads 1
[2023-03-19 00:16:35,084] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:35,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:35,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:35,089] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:35,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:35,090] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.9955	50	1781	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.9003	50	1781	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	74.5865	52	1781	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:35,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17713/tc_result.tsv
[2023-03-19 00:16:35,090] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:35,090] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:35,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference/checkm_data
[2023-03-19 00:16:35,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:35,133] [INFO] Task started: CheckM
[2023-03-19 00:16:35,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17713/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17713/checkm_input OceanDNA-b17713/checkm_result
[2023-03-19 00:17:53,896] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:53,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:53,900] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:53,900] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:53,900] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17713/markers.fasta)
[2023-03-19 00:17:53,902] [INFO] Task started: Blastn
[2023-03-19 00:17:53,902] [INFO] Running command: blastn -query OceanDNA-b17713/markers.fasta -db /var/lib/cwl/stgea891c14-29d8-4d69-b4f4-26fb43f24cc4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17713/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:54,658] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:54,659] [INFO] Selected 32 target genomes.
[2023-03-19 00:17:54,659] [INFO] Target genome list was writen to OceanDNA-b17713/target_genomes_gtdb.txt
[2023-03-19 00:17:54,676] [INFO] Task started: fastANI
[2023-03-19 00:17:54,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgf43ce0ce-cbdf-4c73-9eac-5106b1da1bab/OceanDNA-b17713.fa --refList OceanDNA-b17713/target_genomes_gtdb.txt --output OceanDNA-b17713/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:18:16,830] [INFO] Task succeeded: fastANI
[2023-03-19 00:18:16,835] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:18:16,835] [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_016187725.1	s__SICG01 sp016187725	75.9765	88	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725915.1	s__GCA-2725915 sp002725915	75.8798	97	1781	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_903893785.1	s__CAITNQ01 sp903893785	75.8766	62	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
GCA_016867395.1	s__SICG01 sp016867395	75.7941	100	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018672475.1	s__GCA-2724215 sp018672475	75.7018	54	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
GCA_002726335.1	s__UBA8231 sp002726335	75.6752	110	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673255.1	s__UBA12574 sp018673255	75.3739	88	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660315.1	s__GCA-2724215 sp015660315	75.3721	56	1781	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:18:16,836] [INFO] GTDB search result was written to OceanDNA-b17713/result_gtdb.tsv
[2023-03-19 00:18:16,836] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:18:16,837] [INFO] DFAST_QC result json was written to OceanDNA-b17713/dqc_result.json
[2023-03-19 00:18:16,837] [INFO] DFAST_QC completed!
[2023-03-19 00:18:16,837] [INFO] Total running time: 0h2m35s