[2023-03-18 07:06:20,690] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,691] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference
[2023-03-18 07:06:22,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:22,307] [INFO] Task started: Prodigal
[2023-03-18 07:06:22,307] [INFO] Running command: cat /var/lib/cwl/stgc443918e-2352-4f91-9327-4617b8accb06/OceanDNA-b22184.fa | prodigal -d OceanDNA-b22184/cds.fna -a OceanDNA-b22184/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:33,007] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:33,007] [INFO] Task started: HMMsearch
[2023-03-18 07:06:33,007] [INFO] Running command: hmmsearch --tblout OceanDNA-b22184/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference/reference_markers.hmm OceanDNA-b22184/protein.faa > /dev/null
[2023-03-18 07:06:33,161] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:33,162] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc443918e-2352-4f91-9327-4617b8accb06/OceanDNA-b22184.fa]
[2023-03-18 07:06:33,179] [INFO] Query marker FASTA was written to OceanDNA-b22184/markers.fasta
[2023-03-18 07:06:33,180] [INFO] Task started: Blastn
[2023-03-18 07:06:33,180] [INFO] Running command: blastn -query OceanDNA-b22184/markers.fasta -db /var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference/reference_markers.fasta -out OceanDNA-b22184/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:33,690] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:33,691] [INFO] Selected 15 target genomes.
[2023-03-18 07:06:33,691] [INFO] Target genome list was writen to OceanDNA-b22184/target_genomes.txt
[2023-03-18 07:06:33,698] [INFO] Task started: fastANI
[2023-03-18 07:06:33,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgc443918e-2352-4f91-9327-4617b8accb06/OceanDNA-b22184.fa --refList OceanDNA-b22184/target_genomes.txt --output OceanDNA-b22184/fastani_result.tsv --threads 1
[2023-03-18 07:06:44,708] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:44,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:44,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:44,709] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:44,709] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:44,709] [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
--------------------------------------------------------------------------------
[2023-03-18 07:06:44,709] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22184/tc_result.tsv
[2023-03-18 07:06:44,709] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:44,709] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:44,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference/checkm_data
[2023-03-18 07:06:44,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:44,716] [INFO] Task started: CheckM
[2023-03-18 07:06:44,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22184/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22184/checkm_input OceanDNA-b22184/checkm_result
[2023-03-18 07:07:15,489] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:15,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:15,492] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:15,492] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:15,492] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22184/markers.fasta)
[2023-03-18 07:07:15,493] [INFO] Task started: Blastn
[2023-03-18 07:07:15,493] [INFO] Running command: blastn -query OceanDNA-b22184/markers.fasta -db /var/lib/cwl/stg0160116e-248d-4814-acf1-2ce36f7f646e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22184/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:16,178] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:16,179] [INFO] Selected 10 target genomes.
[2023-03-18 07:07:16,179] [INFO] Target genome list was writen to OceanDNA-b22184/target_genomes_gtdb.txt
[2023-03-18 07:07:16,383] [INFO] Task started: fastANI
[2023-03-18 07:07:16,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgc443918e-2352-4f91-9327-4617b8accb06/OceanDNA-b22184.fa --refList OceanDNA-b22184/target_genomes_gtdb.txt --output OceanDNA-b22184/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:21,455] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:21,461] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:07:21,461] [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_002683195.1	s__GCA-002862325 sp002683195	99.2938	457	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002685335.1	s__GCA-002862325 sp002685335	82.3917	212	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683215.1	s__UBA12014 sp002683215	78.3396	116	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709295.1	s__GCA-002862325 sp002709295	77.9834	174	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167845.2	s__UBA12014 sp002167845	76.7035	95	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.48	99.48	0.92	0.92	2	-
GCA_002862325.1	s__GCA-002862325 sp002862325	76.4492	92	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237965.1	s__UBA12014 sp014237965	76.2434	81	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480395.1	s__UBA12014 sp905480395	76.215	79	495	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:21,461] [INFO] GTDB search result was written to OceanDNA-b22184/result_gtdb.tsv
[2023-03-18 07:07:21,461] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:21,462] [INFO] DFAST_QC result json was written to OceanDNA-b22184/dqc_result.json
[2023-03-18 07:07:21,462] [INFO] DFAST_QC completed!
[2023-03-18 07:07:21,462] [INFO] Total running time: 0h1m1s