[2023-03-15 05:51:32,067] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stg7ad66c51-9863-4645-8282-28a9c783f857/OceanDNA-b13570.fa | prodigal -d OceanDNA-b13570/cds.fna -a OceanDNA-b13570/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:51,851] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:51,852] [INFO] Task started: HMMsearch
[2023-03-15 05:51:51,852] [INFO] Running command: hmmsearch --tblout OceanDNA-b13570/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference/reference_markers.hmm OceanDNA-b13570/protein.faa > /dev/null
[2023-03-15 05:51:52,051] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:52,052] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ad66c51-9863-4645-8282-28a9c783f857/OceanDNA-b13570.fa]
[2023-03-15 05:51:52,075] [INFO] Query marker FASTA was written to OceanDNA-b13570/markers.fasta
[2023-03-15 05:51:52,076] [INFO] Task started: Blastn
[2023-03-15 05:51:52,076] [INFO] Running command: blastn -query OceanDNA-b13570/markers.fasta -db /var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference/reference_markers.fasta -out OceanDNA-b13570/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:52,628] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:52,631] [INFO] Selected 22 target genomes.
[2023-03-15 05:51:52,631] [INFO] Target genome list was writen to OceanDNA-b13570/target_genomes.txt
[2023-03-15 05:51:52,646] [INFO] Task started: fastANI
[2023-03-15 05:51:52,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad66c51-9863-4645-8282-28a9c783f857/OceanDNA-b13570.fa --refList OceanDNA-b13570/target_genomes.txt --output OceanDNA-b13570/fastani_result.tsv --threads 1
[2023-03-15 05:52:07,600] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:07,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:07,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:07,601] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:52:07,601] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:52:07,601] [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
--------------------------------------------------------------------------------
[2023-03-15 05:52:07,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13570/tc_result.tsv
[2023-03-15 05:52:07,605] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:07,605] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:07,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference/checkm_data
[2023-03-15 05:52:07,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:07,614] [INFO] Task started: CheckM
[2023-03-15 05:52:07,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13570/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13570/checkm_input OceanDNA-b13570/checkm_result
[2023-03-15 05:52:55,483] [INFO] Task succeeded: CheckM
[2023-03-15 05:52:55,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:52:55,499] [INFO] ===== Completeness check finished =====
[2023-03-15 05:52:55,499] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:52:55,500] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13570/markers.fasta)
[2023-03-15 05:52:55,501] [INFO] Task started: Blastn
[2023-03-15 05:52:55,501] [INFO] Running command: blastn -query OceanDNA-b13570/markers.fasta -db /var/lib/cwl/stg1fe5556a-65bb-4677-a4af-a622eea36ad0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13570/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:52:56,440] [INFO] Task succeeded: Blastn
[2023-03-15 05:52:56,446] [INFO] Selected 21 target genomes.
[2023-03-15 05:52:56,446] [INFO] Target genome list was writen to OceanDNA-b13570/target_genomes_gtdb.txt
[2023-03-15 05:52:56,469] [INFO] Task started: fastANI
[2023-03-15 05:52:56,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad66c51-9863-4645-8282-28a9c783f857/OceanDNA-b13570.fa --refList OceanDNA-b13570/target_genomes_gtdb.txt --output OceanDNA-b13570/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:10,046] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:10,050] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:53:10,050] [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_018648605.1	s__Desulfolinea sp018648605	99.8157	797	1031	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.90	99.89	0.94	0.91	3	conclusive
GCA_018648685.1	s__Desulfolinea sp018648685	81.052	390	1031	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.60	99.55	0.84	0.83	3	-
GCA_018645405.1	s__Desulfolinea sp018645405	78.6075	346	1031	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.86	99.73	0.91	0.78	10	-
GCA_018648655.1	s__Desulfolinea sp018648655	77.8121	196	1031	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.77	99.77	0.84	0.82	3	-
GCA_014382535.1	s__Desulfolinea nitratireducens	77.7137	220	1031	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.72	99.72	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:10,053] [INFO] GTDB search result was written to OceanDNA-b13570/result_gtdb.tsv
[2023-03-15 05:53:10,055] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:10,058] [INFO] DFAST_QC result json was written to OceanDNA-b13570/dqc_result.json
[2023-03-15 05:53:10,058] [INFO] DFAST_QC completed!
[2023-03-15 05:53:10,058] [INFO] Total running time: 0h1m38s