[2023-03-16 00:33:46,506] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference
[2023-03-16 00:33:47,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,635] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,635] [INFO] Running command: cat /var/lib/cwl/stgc942ee73-3d96-4f08-ad4c-6ef38d31abba/OceanDNA-b26063.fa | prodigal -d OceanDNA-b26063/cds.fna -a OceanDNA-b26063/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:33:56,562] [INFO] Task succeeded: Prodigal
[2023-03-16 00:33:56,562] [INFO] Task started: HMMsearch
[2023-03-16 00:33:56,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b26063/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference/reference_markers.hmm OceanDNA-b26063/protein.faa > /dev/null
[2023-03-16 00:33:56,740] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:33:56,740] [INFO] Found 6/6 markers.
[2023-03-16 00:33:56,755] [INFO] Query marker FASTA was written to OceanDNA-b26063/markers.fasta
[2023-03-16 00:33:56,755] [INFO] Task started: Blastn
[2023-03-16 00:33:56,755] [INFO] Running command: blastn -query OceanDNA-b26063/markers.fasta -db /var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference/reference_markers.fasta -out OceanDNA-b26063/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:33:57,306] [INFO] Task succeeded: Blastn
[2023-03-16 00:33:57,307] [INFO] Selected 24 target genomes.
[2023-03-16 00:33:57,307] [INFO] Target genome list was writen to OceanDNA-b26063/target_genomes.txt
[2023-03-16 00:33:57,604] [INFO] Task started: fastANI
[2023-03-16 00:33:57,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgc942ee73-3d96-4f08-ad4c-6ef38d31abba/OceanDNA-b26063.fa --refList OceanDNA-b26063/target_genomes.txt --output OceanDNA-b26063/fastani_result.tsv --threads 1
[2023-03-16 00:34:08,044] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:08,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:34:08,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:34:08,045] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:34:08,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:34:08,045] [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
--------------------------------------------------------------------------------
[2023-03-16 00:34:08,045] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26063/tc_result.tsv
[2023-03-16 00:34:08,045] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:34:08,046] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:34:08,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference/checkm_data
[2023-03-16 00:34:08,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:34:08,052] [INFO] Task started: CheckM
[2023-03-16 00:34:08,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26063/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26063/checkm_input OceanDNA-b26063/checkm_result
[2023-03-16 00:34:35,014] [INFO] Task succeeded: CheckM
[2023-03-16 00:34:35,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:34:35,026] [INFO] ===== Completeness check finished =====
[2023-03-16 00:34:35,026] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:34:35,026] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26063/markers.fasta)
[2023-03-16 00:34:35,027] [INFO] Task started: Blastn
[2023-03-16 00:34:35,028] [INFO] Running command: blastn -query OceanDNA-b26063/markers.fasta -db /var/lib/cwl/stg94b5a0c7-003e-495b-97c9-24e77e813ce1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26063/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:35,923] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:35,924] [INFO] Selected 11 target genomes.
[2023-03-16 00:34:35,924] [INFO] Target genome list was writen to OceanDNA-b26063/target_genomes_gtdb.txt
[2023-03-16 00:34:36,017] [INFO] Task started: fastANI
[2023-03-16 00:34:36,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgc942ee73-3d96-4f08-ad4c-6ef38d31abba/OceanDNA-b26063.fa --refList OceanDNA-b26063/target_genomes_gtdb.txt --output OceanDNA-b26063/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:34:39,571] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:39,578] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:34:39,578] [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_004213885.1	s__TMED54 sp004213885	99.6723	391	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902618195.1	s__TMED54 sp902618195	93.1533	267	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630555.1	s__TMED54 sp902630555	92.8008	226	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902550555.1	s__TMED54 sp902550555	92.1113	365	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615025.1	s__TMED54 sp902615025	92.0169	329	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615995.1	s__TMED54 sp902615995	92.0011	289	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622745.1	s__TMED54 sp902622745	90.9958	301	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210115.1	s__TMED54 sp003210115	90.5412	254	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902524215.1	s__TMED54 sp902524215	90.1577	277	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616005.1	s__TMED54 sp902616005	89.6464	387	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615325.1	s__TMED54 sp902615325	89.0127	397	592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__TMED54	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:34:39,578] [INFO] GTDB search result was written to OceanDNA-b26063/result_gtdb.tsv
[2023-03-16 00:34:39,578] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:34:39,579] [INFO] DFAST_QC result json was written to OceanDNA-b26063/dqc_result.json
[2023-03-16 00:34:39,579] [INFO] DFAST_QC completed!
[2023-03-16 00:34:39,579] [INFO] Total running time: 0h0m53s