[2023-03-18 07:29:30,338] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,338] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg15090c16-9fbe-4f6f-bcf4-66f3b3b3d484/OceanDNA-b12880.fa | prodigal -d OceanDNA-b12880/cds.fna -a OceanDNA-b12880/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:48,067] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:48,067] [INFO] Task started: HMMsearch
[2023-03-18 07:29:48,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b12880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference/reference_markers.hmm OceanDNA-b12880/protein.faa > /dev/null
[2023-03-18 07:29:48,247] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:48,248] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15090c16-9fbe-4f6f-bcf4-66f3b3b3d484/OceanDNA-b12880.fa]
[2023-03-18 07:29:48,260] [INFO] Query marker FASTA was written to OceanDNA-b12880/markers.fasta
[2023-03-18 07:29:48,261] [INFO] Task started: Blastn
[2023-03-18 07:29:48,261] [INFO] Running command: blastn -query OceanDNA-b12880/markers.fasta -db /var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference/reference_markers.fasta -out OceanDNA-b12880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:48,831] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:48,831] [INFO] Selected 25 target genomes.
[2023-03-18 07:29:48,832] [INFO] Target genome list was writen to OceanDNA-b12880/target_genomes.txt
[2023-03-18 07:29:48,844] [INFO] Task started: fastANI
[2023-03-18 07:29:48,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg15090c16-9fbe-4f6f-bcf4-66f3b3b3d484/OceanDNA-b12880.fa --refList OceanDNA-b12880/target_genomes.txt --output OceanDNA-b12880/fastani_result.tsv --threads 1
[2023-03-18 07:30:10,092] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:10,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:10,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:10,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:10,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:30:10,093] [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 07:30:10,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12880/tc_result.tsv
[2023-03-18 07:30:10,093] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:10,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:10,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference/checkm_data
[2023-03-18 07:30:10,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:10,099] [INFO] Task started: CheckM
[2023-03-18 07:30:10,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12880/checkm_input OceanDNA-b12880/checkm_result
[2023-03-18 07:30:53,481] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:53,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 7.81%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-18 07:30:53,483] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:53,484] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:53,484] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12880/markers.fasta)
[2023-03-18 07:30:53,484] [INFO] Task started: Blastn
[2023-03-18 07:30:53,484] [INFO] Running command: blastn -query OceanDNA-b12880/markers.fasta -db /var/lib/cwl/stg6d36d7b0-7b25-421f-9394-e6c7627bbcba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:54,323] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:54,324] [INFO] Selected 17 target genomes.
[2023-03-18 07:30:54,324] [INFO] Target genome list was writen to OceanDNA-b12880/target_genomes_gtdb.txt
[2023-03-18 07:30:54,540] [INFO] Task started: fastANI
[2023-03-18 07:30:54,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg15090c16-9fbe-4f6f-bcf4-66f3b3b3d484/OceanDNA-b12880.fa --refList OceanDNA-b12880/target_genomes_gtdb.txt --output OceanDNA-b12880/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:02,177] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:02,182] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:31:02,182] [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_009926405.1	s__SYHX01 sp009926405	99.5058	335	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903856555.1	s__SYHX01 sp903856555	84.3585	403	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	99.26	99.23	0.85	0.84	3	-
GCA_009926245.1	s__SYHX01 sp009926245	83.1573	315	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	98.28	98.28	0.87	0.87	2	-
GCA_009927485.1	s__SYHX01 sp009927485	79.5885	133	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	98.38	98.38	0.80	0.80	2	-
GCA_016872125.1	s__SYHX01 sp016872125	78.7649	102	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005799025.1	s__SYHX01 sp005799025	78.7578	129	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868875.1	s__SYHX01 sp016868875	78.1083	91	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__SYHX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:02,182] [INFO] GTDB search result was written to OceanDNA-b12880/result_gtdb.tsv
[2023-03-18 07:31:02,182] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:02,183] [INFO] DFAST_QC result json was written to OceanDNA-b12880/dqc_result.json
[2023-03-18 07:31:02,183] [INFO] DFAST_QC completed!
[2023-03-18 07:31:02,183] [INFO] Total running time: 0h1m32s