[2023-03-15 11:54:50,869] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:54:50,869] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:54:50,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference
[2023-03-15 11:54:51,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:54:51,950] [INFO] Task started: Prodigal
[2023-03-15 11:54:51,950] [INFO] Running command: cat /var/lib/cwl/stg948065f6-684c-43ab-b12b-4c1306685c7d/OceanDNA-b29622.fa | prodigal -d OceanDNA-b29622/cds.fna -a OceanDNA-b29622/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:54:58,319] [INFO] Task succeeded: Prodigal
[2023-03-15 11:54:58,319] [INFO] Task started: HMMsearch
[2023-03-15 11:54:58,319] [INFO] Running command: hmmsearch --tblout OceanDNA-b29622/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference/reference_markers.hmm OceanDNA-b29622/protein.faa > /dev/null
[2023-03-15 11:54:58,464] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:54:58,465] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg948065f6-684c-43ab-b12b-4c1306685c7d/OceanDNA-b29622.fa]
[2023-03-15 11:54:58,480] [INFO] Query marker FASTA was written to OceanDNA-b29622/markers.fasta
[2023-03-15 11:54:58,480] [INFO] Task started: Blastn
[2023-03-15 11:54:58,480] [INFO] Running command: blastn -query OceanDNA-b29622/markers.fasta -db /var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference/reference_markers.fasta -out OceanDNA-b29622/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:54:59,020] [INFO] Task succeeded: Blastn
[2023-03-15 11:54:59,022] [INFO] Selected 22 target genomes.
[2023-03-15 11:54:59,022] [INFO] Target genome list was writen to OceanDNA-b29622/target_genomes.txt
[2023-03-15 11:54:59,034] [INFO] Task started: fastANI
[2023-03-15 11:54:59,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg948065f6-684c-43ab-b12b-4c1306685c7d/OceanDNA-b29622.fa --refList OceanDNA-b29622/target_genomes.txt --output OceanDNA-b29622/fastani_result.tsv --threads 1
[2023-03-15 11:55:11,815] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:11,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:55:11,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:55:11,820] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:55:11,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:55:11,820] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	86.4173	244	258	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:55:11,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29622/tc_result.tsv
[2023-03-15 11:55:11,825] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:55:11,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:55:11,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference/checkm_data
[2023-03-15 11:55:11,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:55:11,832] [INFO] Task started: CheckM
[2023-03-15 11:55:11,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29622/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29622/checkm_input OceanDNA-b29622/checkm_result
[2023-03-15 11:55:34,111] [INFO] Task succeeded: CheckM
[2023-03-15 11:55:34,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.75%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:55:34,142] [INFO] ===== Completeness check finished =====
[2023-03-15 11:55:34,142] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:55:34,142] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29622/markers.fasta)
[2023-03-15 11:55:34,144] [INFO] Task started: Blastn
[2023-03-15 11:55:34,144] [INFO] Running command: blastn -query OceanDNA-b29622/markers.fasta -db /var/lib/cwl/stg7d7e6516-d2ca-4e81-af9a-da07b31cc4a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29622/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:55:34,938] [INFO] Task succeeded: Blastn
[2023-03-15 11:55:34,947] [INFO] Selected 12 target genomes.
[2023-03-15 11:55:34,947] [INFO] Target genome list was writen to OceanDNA-b29622/target_genomes_gtdb.txt
[2023-03-15 11:55:34,963] [INFO] Task started: fastANI
[2023-03-15 11:55:34,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg948065f6-684c-43ab-b12b-4c1306685c7d/OceanDNA-b29622.fa --refList OceanDNA-b29622/target_genomes_gtdb.txt --output OceanDNA-b29622/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:55:40,084] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:40,088] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:55:40,088] [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_905181815.1	s__Planktomarina sp905181815	86.6676	228	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738435.1	s__Planktomarina temperata	86.4173	244	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	-
GCA_016780825.1	s__Planktomarina sp016780825	86.1806	218	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683685.1	s__Planktomarina sp002683685	84.3396	180	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	-
GCA_905182455.1	s__Planktomarina sp905182455	78.0198	89	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:55:40,089] [INFO] GTDB search result was written to OceanDNA-b29622/result_gtdb.tsv
[2023-03-15 11:55:40,091] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:55:40,094] [INFO] DFAST_QC result json was written to OceanDNA-b29622/dqc_result.json
[2023-03-15 11:55:40,094] [INFO] DFAST_QC completed!
[2023-03-15 11:55:40,094] [INFO] Total running time: 0h0m49s