[2023-03-17 07:01:49,599] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference
[2023-03-17 07:01:51,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,529] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,529] [INFO] Running command: cat /var/lib/cwl/stg676d0624-1074-449c-9713-68c1c5c0cfd2/OceanDNA-b15181.fa | prodigal -d OceanDNA-b15181/cds.fna -a OceanDNA-b15181/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:54,376] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:54,377] [INFO] Task started: HMMsearch
[2023-03-17 07:01:54,377] [INFO] Running command: hmmsearch --tblout OceanDNA-b15181/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference/reference_markers.hmm OceanDNA-b15181/protein.faa > /dev/null
[2023-03-17 07:01:54,567] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:54,568] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg676d0624-1074-449c-9713-68c1c5c0cfd2/OceanDNA-b15181.fa]
[2023-03-17 07:01:54,573] [INFO] Query marker FASTA was written to OceanDNA-b15181/markers.fasta
[2023-03-17 07:01:54,575] [INFO] Task started: Blastn
[2023-03-17 07:01:54,575] [INFO] Running command: blastn -query OceanDNA-b15181/markers.fasta -db /var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference/reference_markers.fasta -out OceanDNA-b15181/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:01:57,781] [INFO] Task succeeded: Blastn
[2023-03-17 07:01:57,781] [INFO] Selected 5 target genomes.
[2023-03-17 07:01:57,782] [INFO] Target genome list was writen to OceanDNA-b15181/target_genomes.txt
[2023-03-17 07:01:57,785] [INFO] Task started: fastANI
[2023-03-17 07:01:57,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg676d0624-1074-449c-9713-68c1c5c0cfd2/OceanDNA-b15181.fa --refList OceanDNA-b15181/target_genomes.txt --output OceanDNA-b15181/fastani_result.tsv --threads 1
[2023-03-17 07:01:58,934] [INFO] Task succeeded: fastANI
[2023-03-17 07:01:58,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:01:58,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:01:58,935] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:01:58,935] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:01:58,935] [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 07:01:58,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15181/tc_result.tsv
[2023-03-17 07:01:58,935] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:01:58,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:01:58,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference/checkm_data
[2023-03-17 07:01:58,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:01:59,421] [INFO] Task started: CheckM
[2023-03-17 07:01:59,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15181/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15181/checkm_input OceanDNA-b15181/checkm_result
[2023-03-17 07:02:17,779] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:17,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:17,781] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:17,781] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:17,781] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15181/markers.fasta)
[2023-03-17 07:02:17,783] [INFO] Task started: Blastn
[2023-03-17 07:02:17,783] [INFO] Running command: blastn -query OceanDNA-b15181/markers.fasta -db /var/lib/cwl/stgfda2f501-eea6-41eb-a93a-6d0499ca584d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15181/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:18,571] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:18,572] [INFO] Selected 12 target genomes.
[2023-03-17 07:02:18,572] [INFO] Target genome list was writen to OceanDNA-b15181/target_genomes_gtdb.txt
[2023-03-17 07:02:18,965] [INFO] Task started: fastANI
[2023-03-17 07:02:18,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg676d0624-1074-449c-9713-68c1c5c0cfd2/OceanDNA-b15181.fa --refList OceanDNA-b15181/target_genomes_gtdb.txt --output OceanDNA-b15181/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:21,389] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:21,392] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:02:21,392] [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_002718395.1	s__GCA-002718395 sp002718395	99.9502	110	179	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__GCA-002718395	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002710905.1	s__GCA-002718395 sp002710905	83.6963	121	179	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__GCA-002718395	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228125.1	s__GCA-002718395 sp003228125	75.9885	51	179	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__GCA-002718395	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:21,392] [INFO] GTDB search result was written to OceanDNA-b15181/result_gtdb.tsv
[2023-03-17 07:02:21,392] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:21,393] [INFO] DFAST_QC result json was written to OceanDNA-b15181/dqc_result.json
[2023-03-17 07:02:21,393] [INFO] DFAST_QC completed!
[2023-03-17 07:02:21,393] [INFO] Total running time: 0h0m32s