[2023-03-18 22:44:58,033] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:58,033] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:58,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference
[2023-03-18 22:44:59,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,116] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,116] [INFO] Running command: cat /var/lib/cwl/stg76942da3-9ec8-40d1-8776-bb18d7b3cca6/OceanDNA-b17223.fa | prodigal -d OceanDNA-b17223/cds.fna -a OceanDNA-b17223/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:18,854] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:18,855] [INFO] Task started: HMMsearch
[2023-03-18 22:45:18,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b17223/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference/reference_markers.hmm OceanDNA-b17223/protein.faa > /dev/null
[2023-03-18 22:45:19,033] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:19,034] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg76942da3-9ec8-40d1-8776-bb18d7b3cca6/OceanDNA-b17223.fa]
[2023-03-18 22:45:19,071] [INFO] Query marker FASTA was written to OceanDNA-b17223/markers.fasta
[2023-03-18 22:45:19,072] [INFO] Task started: Blastn
[2023-03-18 22:45:19,072] [INFO] Running command: blastn -query OceanDNA-b17223/markers.fasta -db /var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference/reference_markers.fasta -out OceanDNA-b17223/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:19,608] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:19,616] [INFO] Selected 22 target genomes.
[2023-03-18 22:45:19,617] [INFO] Target genome list was writen to OceanDNA-b17223/target_genomes.txt
[2023-03-18 22:45:19,630] [INFO] Task started: fastANI
[2023-03-18 22:45:19,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg76942da3-9ec8-40d1-8776-bb18d7b3cca6/OceanDNA-b17223.fa --refList OceanDNA-b17223/target_genomes.txt --output OceanDNA-b17223/fastani_result.tsv --threads 1
[2023-03-18 22:45:35,403] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:35,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:35,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:35,408] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:35,408] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:45:35,408] [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	75.051	68	1067	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	74.6131	54	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:45:35,410] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17223/tc_result.tsv
[2023-03-18 22:45:35,413] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:35,413] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:35,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference/checkm_data
[2023-03-18 22:45:35,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:35,480] [INFO] Task started: CheckM
[2023-03-18 22:45:35,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17223/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17223/checkm_input OceanDNA-b17223/checkm_result
[2023-03-18 22:46:25,339] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:25,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:25,449] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:25,450] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:25,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17223/markers.fasta)
[2023-03-18 22:46:25,451] [INFO] Task started: Blastn
[2023-03-18 22:46:25,451] [INFO] Running command: blastn -query OceanDNA-b17223/markers.fasta -db /var/lib/cwl/stg3c04f014-9f17-42b4-bac9-6d6d0686bf7c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17223/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:26,248] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:26,300] [INFO] Selected 13 target genomes.
[2023-03-18 22:46:26,300] [INFO] Target genome list was writen to OceanDNA-b17223/target_genomes_gtdb.txt
[2023-03-18 22:46:26,345] [INFO] Task started: fastANI
[2023-03-18 22:46:26,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg76942da3-9ec8-40d1-8776-bb18d7b3cca6/OceanDNA-b17223.fa --refList OceanDNA-b17223/target_genomes_gtdb.txt --output OceanDNA-b17223/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:46:34,804] [INFO] Task succeeded: fastANI
[2023-03-18 22:46:34,810] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:46:34,811] [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_015664885.1	s__UBA1138 sp003447875	76.8967	219	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_016873995.1	s__UBA2982 sp016873995	76.8461	126	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692205.1	s__UBA2982 sp009692205	76.5896	141	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937285.1	s__UBA1138 sp009937285	76.263	95	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.12	98.44	0.93	0.79	16	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.1459	146	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	76.0923	114	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_009840215.1	s__Bin94 sp009840215	75.9787	68	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.38	99.00	0.93	0.91	6	-
GCA_002390225.1	s__UBA2589 sp002390225	75.9215	101	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838975.1	s__Bin94 sp009838975	75.5672	74	1067	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.37	98.63	0.95	0.92	5	-
--------------------------------------------------------------------------------
[2023-03-18 22:46:34,832] [INFO] GTDB search result was written to OceanDNA-b17223/result_gtdb.tsv
[2023-03-18 22:46:34,867] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:46:34,877] [INFO] DFAST_QC result json was written to OceanDNA-b17223/dqc_result.json
[2023-03-18 22:46:34,877] [INFO] DFAST_QC completed!
[2023-03-18 22:46:34,877] [INFO] Total running time: 0h1m37s