[2023-03-17 00:45:47,246] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,246] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg57fe788b-d94e-497c-8328-4a431d0e901f/OceanDNA-b12210.fa | prodigal -d OceanDNA-b12210/cds.fna -a OceanDNA-b12210/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:58,020] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:58,020] [INFO] Task started: HMMsearch
[2023-03-17 00:45:58,020] [INFO] Running command: hmmsearch --tblout OceanDNA-b12210/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference/reference_markers.hmm OceanDNA-b12210/protein.faa > /dev/null
[2023-03-17 00:45:58,175] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:58,175] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg57fe788b-d94e-497c-8328-4a431d0e901f/OceanDNA-b12210.fa]
[2023-03-17 00:45:58,189] [INFO] Query marker FASTA was written to OceanDNA-b12210/markers.fasta
[2023-03-17 00:45:58,189] [INFO] Task started: Blastn
[2023-03-17 00:45:58,189] [INFO] Running command: blastn -query OceanDNA-b12210/markers.fasta -db /var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference/reference_markers.fasta -out OceanDNA-b12210/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:58,685] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:58,686] [INFO] Selected 17 target genomes.
[2023-03-17 00:45:58,686] [INFO] Target genome list was writen to OceanDNA-b12210/target_genomes.txt
[2023-03-17 00:45:58,779] [INFO] Task started: fastANI
[2023-03-17 00:45:58,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg57fe788b-d94e-497c-8328-4a431d0e901f/OceanDNA-b12210.fa --refList OceanDNA-b12210/target_genomes.txt --output OceanDNA-b12210/fastani_result.tsv --threads 1
[2023-03-17 00:46:07,701] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:07,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:07,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:07,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:07,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:07,702] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:07,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12210/tc_result.tsv
[2023-03-17 00:46:07,702] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:07,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:07,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference/checkm_data
[2023-03-17 00:46:07,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:07,709] [INFO] Task started: CheckM
[2023-03-17 00:46:07,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12210/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12210/checkm_input OceanDNA-b12210/checkm_result
[2023-03-17 00:46:36,754] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:36,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:36,756] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:36,756] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:36,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12210/markers.fasta)
[2023-03-17 00:46:36,758] [INFO] Task started: Blastn
[2023-03-17 00:46:36,758] [INFO] Running command: blastn -query OceanDNA-b12210/markers.fasta -db /var/lib/cwl/stg86f31d17-592e-4726-a32f-cd902e752190/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12210/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:37,416] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:37,417] [INFO] Selected 14 target genomes.
[2023-03-17 00:46:37,417] [INFO] Target genome list was writen to OceanDNA-b12210/target_genomes_gtdb.txt
[2023-03-17 00:46:37,699] [INFO] Task started: fastANI
[2023-03-17 00:46:37,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg57fe788b-d94e-497c-8328-4a431d0e901f/OceanDNA-b12210.fa --refList OceanDNA-b12210/target_genomes_gtdb.txt --output OceanDNA-b12210/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:42,946] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:42,952] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:46:42,953] [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_002727735.1	s__GCA-002727735 sp002727735	97.2284	343	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002694645.1	s__GCA-002727735 sp002694645	77.4	75	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780365.1	s__MED-G20 sp016780365	76.3865	63	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_905181675.1	s__MED-G20 sp905181675	76.3419	50	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723085.1	s__GCA-2723085 sp002723085	76.2917	92	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713405.1	s__MED-G20 sp002713405	76.1712	65	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182525.1	s__MED-G20 sp905182525	76.1534	79	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:43,074] [INFO] GTDB search result was written to OceanDNA-b12210/result_gtdb.tsv
[2023-03-17 00:46:43,074] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:43,075] [INFO] DFAST_QC result json was written to OceanDNA-b12210/dqc_result.json
[2023-03-17 00:46:43,076] [INFO] DFAST_QC completed!
[2023-03-17 00:46:43,076] [INFO] Total running time: 0h0m56s