[2023-03-19 02:59:38,306] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,306] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference
[2023-03-19 02:59:39,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,379] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,379] [INFO] Running command: cat /var/lib/cwl/stgc80b2d79-282b-4f68-83eb-f3ad7664a380/OceanDNA-b19786.fa | prodigal -d OceanDNA-b19786/cds.fna -a OceanDNA-b19786/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:59:47,381] [INFO] Task succeeded: Prodigal
[2023-03-19 02:59:47,382] [INFO] Task started: HMMsearch
[2023-03-19 02:59:47,382] [INFO] Running command: hmmsearch --tblout OceanDNA-b19786/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference/reference_markers.hmm OceanDNA-b19786/protein.faa > /dev/null
[2023-03-19 02:59:47,529] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:59:47,529] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc80b2d79-282b-4f68-83eb-f3ad7664a380/OceanDNA-b19786.fa]
[2023-03-19 02:59:47,542] [INFO] Query marker FASTA was written to OceanDNA-b19786/markers.fasta
[2023-03-19 02:59:47,542] [INFO] Task started: Blastn
[2023-03-19 02:59:47,542] [INFO] Running command: blastn -query OceanDNA-b19786/markers.fasta -db /var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference/reference_markers.fasta -out OceanDNA-b19786/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:59:48,605] [INFO] Task succeeded: Blastn
[2023-03-19 02:59:48,606] [INFO] Selected 12 target genomes.
[2023-03-19 02:59:48,606] [INFO] Target genome list was writen to OceanDNA-b19786/target_genomes.txt
[2023-03-19 02:59:48,611] [INFO] Task started: fastANI
[2023-03-19 02:59:48,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80b2d79-282b-4f68-83eb-f3ad7664a380/OceanDNA-b19786.fa --refList OceanDNA-b19786/target_genomes.txt --output OceanDNA-b19786/fastani_result.tsv --threads 1
[2023-03-19 02:59:54,032] [INFO] Task succeeded: fastANI
[2023-03-19 02:59:54,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:59:54,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:59:54,032] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:59:54,032] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:59:54,032] [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
--------------------------------------------------------------------------------
[2023-03-19 02:59:54,033] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19786/tc_result.tsv
[2023-03-19 02:59:54,033] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:59:54,033] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:59:54,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference/checkm_data
[2023-03-19 02:59:54,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:59:54,201] [INFO] Task started: CheckM
[2023-03-19 02:59:54,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19786/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19786/checkm_input OceanDNA-b19786/checkm_result
[2023-03-19 03:00:19,423] [INFO] Task succeeded: CheckM
[2023-03-19 03:00:19,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 03:00:19,426] [INFO] ===== Completeness check finished =====
[2023-03-19 03:00:19,426] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:00:19,426] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19786/markers.fasta)
[2023-03-19 03:00:19,426] [INFO] Task started: Blastn
[2023-03-19 03:00:19,426] [INFO] Running command: blastn -query OceanDNA-b19786/markers.fasta -db /var/lib/cwl/stgb3b33eb5-c142-46b4-8b28-e971eddb0fdf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19786/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:19,873] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:19,874] [INFO] Selected 17 target genomes.
[2023-03-19 03:00:19,874] [INFO] Target genome list was writen to OceanDNA-b19786/target_genomes_gtdb.txt
[2023-03-19 03:00:19,889] [INFO] Task started: fastANI
[2023-03-19 03:00:19,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80b2d79-282b-4f68-83eb-f3ad7664a380/OceanDNA-b19786.fa --refList OceanDNA-b19786/target_genomes_gtdb.txt --output OceanDNA-b19786/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:00:25,465] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:25,469] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:00:25,469] [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_002698235.1	s__GCA-002718655 sp002698235	82.348	341	491	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002718655	95.0	97.12	97.12	0.77	0.77	2	-
GCA_902562835.1	s__CACEUX01 sp902562835	76.9163	72	491	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718655.1	s__GCA-002718655 sp002718655	76.8085	69	491	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002718655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167345.2	s__CACEUX01 sp002167345	76.5812	86	491	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708715.1	s__GCA-002708715 sp002708715	76.3805	67	491	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:00:25,469] [INFO] GTDB search result was written to OceanDNA-b19786/result_gtdb.tsv
[2023-03-19 03:00:25,469] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:00:25,470] [INFO] DFAST_QC result json was written to OceanDNA-b19786/dqc_result.json
[2023-03-19 03:00:25,470] [INFO] DFAST_QC completed!
[2023-03-19 03:00:25,470] [INFO] Total running time: 0h0m47s