[2023-03-18 10:32:24,476] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:32:24,476] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:32:24,476] [INFO] DQC Reference Directory: /var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference
[2023-03-18 10:32:25,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:32:25,617] [INFO] Task started: Prodigal
[2023-03-18 10:32:25,617] [INFO] Running command: cat /var/lib/cwl/stg4175f854-cc23-42c7-85bf-81d965ca42af/OceanDNA-a1636.fa | prodigal -d OceanDNA-a1636/cds.fna -a OceanDNA-a1636/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:32:29,923] [INFO] Task succeeded: Prodigal
[2023-03-18 10:32:29,923] [INFO] Task started: HMMsearch
[2023-03-18 10:32:29,923] [INFO] Running command: hmmsearch --tblout OceanDNA-a1636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference/reference_markers.hmm OceanDNA-a1636/protein.faa > /dev/null
[2023-03-18 10:32:30,095] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:32:30,096] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4175f854-cc23-42c7-85bf-81d965ca42af/OceanDNA-a1636.fa]
[2023-03-18 10:32:30,109] [INFO] Query marker FASTA was written to OceanDNA-a1636/markers.fasta
[2023-03-18 10:32:30,111] [INFO] Task started: Blastn
[2023-03-18 10:32:30,111] [INFO] Running command: blastn -query OceanDNA-a1636/markers.fasta -db /var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference/reference_markers.fasta -out OceanDNA-a1636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:32:30,730] [INFO] Task succeeded: Blastn
[2023-03-18 10:32:30,732] [INFO] Selected 10 target genomes.
[2023-03-18 10:32:30,732] [INFO] Target genome list was writen to OceanDNA-a1636/target_genomes.txt
[2023-03-18 10:32:30,766] [INFO] Task started: fastANI
[2023-03-18 10:32:30,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg4175f854-cc23-42c7-85bf-81d965ca42af/OceanDNA-a1636.fa --refList OceanDNA-a1636/target_genomes.txt --output OceanDNA-a1636/fastani_result.tsv --threads 1
[2023-03-18 10:32:34,665] [INFO] Task succeeded: fastANI
[2023-03-18 10:32:34,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:32:34,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:32:34,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:32:34,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:32:34,666] [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 10:32:34,668] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1636/tc_result.tsv
[2023-03-18 10:32:34,668] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:32:34,668] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:32:34,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference/checkm_data
[2023-03-18 10:32:34,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:32:34,900] [INFO] Task started: CheckM
[2023-03-18 10:32:34,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1636/checkm_input OceanDNA-a1636/checkm_result
[2023-03-18 10:32:54,492] [INFO] Task succeeded: CheckM
[2023-03-18 10:32:54,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.10%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 10:32:54,497] [INFO] ===== Completeness check finished =====
[2023-03-18 10:32:54,497] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:32:54,497] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1636/markers.fasta)
[2023-03-18 10:32:54,499] [INFO] Task started: Blastn
[2023-03-18 10:32:54,499] [INFO] Running command: blastn -query OceanDNA-a1636/markers.fasta -db /var/lib/cwl/stge1d575d1-a105-4c54-af92-5e554c8d3d84/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:32:55,305] [INFO] Task succeeded: Blastn
[2023-03-18 10:32:55,306] [INFO] Selected 10 target genomes.
[2023-03-18 10:32:55,307] [INFO] Target genome list was writen to OceanDNA-a1636/target_genomes_gtdb.txt
[2023-03-18 10:32:55,314] [INFO] Task started: fastANI
[2023-03-18 10:32:55,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg4175f854-cc23-42c7-85bf-81d965ca42af/OceanDNA-a1636.fa --refList OceanDNA-a1636/target_genomes_gtdb.txt --output OceanDNA-a1636/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:32:57,130] [INFO] Task succeeded: fastANI
[2023-03-18 10:32:57,136] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:32:57,136] [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_902627615.1	s__CG-Epi1 sp902627615	89.562	196	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531985.1	s__CG-Epi1 sp902531985	87.128	139	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533295.1	s__CG-Epi1 sp902533295	79.4434	86	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240255.1	s__CG-Epi1 sp014240255	77.7952	83	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718915.1	s__CG-Epi1 sp002718915	77.7773	61	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240055.1	s__CG-Epi1 sp014240055	77.5414	79	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875345.1	s__CG-Epi1 sp001875345	77.4373	64	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	77.3271	64	229	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:32:57,137] [INFO] GTDB search result was written to OceanDNA-a1636/result_gtdb.tsv
[2023-03-18 10:32:57,137] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:32:57,139] [INFO] DFAST_QC result json was written to OceanDNA-a1636/dqc_result.json
[2023-03-18 10:32:57,139] [INFO] DFAST_QC completed!
[2023-03-18 10:32:57,139] [INFO] Total running time: 0h0m33s