[2023-03-17 02:54:22,029] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:54:22,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:54:22,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference
[2023-03-17 02:54:23,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:54:23,266] [INFO] Task started: Prodigal
[2023-03-17 02:54:23,266] [INFO] Running command: cat /var/lib/cwl/stg6c39e213-806f-41bb-8452-d07aceab4a62/OceanDNA-a1887.fa | prodigal -d OceanDNA-a1887/cds.fna -a OceanDNA-a1887/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:54:31,767] [INFO] Task succeeded: Prodigal
[2023-03-17 02:54:31,768] [INFO] Task started: HMMsearch
[2023-03-17 02:54:31,768] [INFO] Running command: hmmsearch --tblout OceanDNA-a1887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference/reference_markers.hmm OceanDNA-a1887/protein.faa > /dev/null
[2023-03-17 02:54:31,929] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:54:31,930] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6c39e213-806f-41bb-8452-d07aceab4a62/OceanDNA-a1887.fa]
[2023-03-17 02:54:31,945] [INFO] Query marker FASTA was written to OceanDNA-a1887/markers.fasta
[2023-03-17 02:54:31,947] [INFO] Task started: Blastn
[2023-03-17 02:54:31,947] [INFO] Running command: blastn -query OceanDNA-a1887/markers.fasta -db /var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference/reference_markers.fasta -out OceanDNA-a1887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:54:32,639] [INFO] Task succeeded: Blastn
[2023-03-17 02:54:32,643] [INFO] Selected 5 target genomes.
[2023-03-17 02:54:32,643] [INFO] Target genome list was writen to OceanDNA-a1887/target_genomes.txt
[2023-03-17 02:54:32,654] [INFO] Task started: fastANI
[2023-03-17 02:54:32,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c39e213-806f-41bb-8452-d07aceab4a62/OceanDNA-a1887.fa --refList OceanDNA-a1887/target_genomes.txt --output OceanDNA-a1887/fastani_result.tsv --threads 1
[2023-03-17 02:54:35,589] [INFO] Task succeeded: fastANI
[2023-03-17 02:54:35,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:54:35,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:54:35,590] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:54:35,590] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:54:35,590] [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 02:54:35,592] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1887/tc_result.tsv
[2023-03-17 02:54:35,593] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:54:35,593] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:54:35,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference/checkm_data
[2023-03-17 02:54:35,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:54:35,645] [INFO] Task started: CheckM
[2023-03-17 02:54:35,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1887/checkm_input OceanDNA-a1887/checkm_result
[2023-03-17 02:55:06,110] [INFO] Task succeeded: CheckM
[2023-03-17 02:55:06,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.63%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:55:06,117] [INFO] ===== Completeness check finished =====
[2023-03-17 02:55:06,118] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:55:06,118] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1887/markers.fasta)
[2023-03-17 02:55:06,120] [INFO] Task started: Blastn
[2023-03-17 02:55:06,120] [INFO] Running command: blastn -query OceanDNA-a1887/markers.fasta -db /var/lib/cwl/stg6f47cbd8-ad58-47be-880e-c70898ec9be4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:55:07,194] [INFO] Task succeeded: Blastn
[2023-03-17 02:55:07,197] [INFO] Selected 9 target genomes.
[2023-03-17 02:55:07,197] [INFO] Target genome list was writen to OceanDNA-a1887/target_genomes_gtdb.txt
[2023-03-17 02:55:07,202] [INFO] Task started: fastANI
[2023-03-17 02:55:07,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c39e213-806f-41bb-8452-d07aceab4a62/OceanDNA-a1887.fa --refList OceanDNA-a1887/target_genomes_gtdb.txt --output OceanDNA-a1887/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:55:09,909] [INFO] Task succeeded: fastANI
[2023-03-17 02:55:09,913] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:55:09,913] [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_002689565.1	s__MGIIa-K1 sp002689565	81.0405	203	500	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	78.0915	135	500	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_002715725.1	s__MGIIa-K1 sp002715725	78.0554	157	500	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.59	99.59	0.80	0.80	2	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	77.9643	152	500	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706615.1	s__MGIIa-K1 sp002706615	76.1933	51	500	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.10	98.10	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:55:09,915] [INFO] GTDB search result was written to OceanDNA-a1887/result_gtdb.tsv
[2023-03-17 02:55:09,915] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:55:09,917] [INFO] DFAST_QC result json was written to OceanDNA-a1887/dqc_result.json
[2023-03-17 02:55:09,917] [INFO] DFAST_QC completed!
[2023-03-17 02:55:09,917] [INFO] Total running time: 0h0m48s