[2023-03-18 02:27:37,198] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,198] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,198] [INFO] DQC Reference Directory: /var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference
[2023-03-18 02:27:38,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stgad8b95b4-7f0b-41e5-9c0f-9b47c48bb8fe/OceanDNA-b23261.fa | prodigal -d OceanDNA-b23261/cds.fna -a OceanDNA-b23261/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:02,481] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:02,481] [INFO] Task started: HMMsearch
[2023-03-18 02:28:02,481] [INFO] Running command: hmmsearch --tblout OceanDNA-b23261/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference/reference_markers.hmm OceanDNA-b23261/protein.faa > /dev/null
[2023-03-18 02:28:02,766] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:02,767] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgad8b95b4-7f0b-41e5-9c0f-9b47c48bb8fe/OceanDNA-b23261.fa]
[2023-03-18 02:28:02,789] [INFO] Query marker FASTA was written to OceanDNA-b23261/markers.fasta
[2023-03-18 02:28:02,789] [INFO] Task started: Blastn
[2023-03-18 02:28:02,789] [INFO] Running command: blastn -query OceanDNA-b23261/markers.fasta -db /var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference/reference_markers.fasta -out OceanDNA-b23261/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:03,425] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:03,426] [INFO] Selected 27 target genomes.
[2023-03-18 02:28:03,426] [INFO] Target genome list was writen to OceanDNA-b23261/target_genomes.txt
[2023-03-18 02:28:03,440] [INFO] Task started: fastANI
[2023-03-18 02:28:03,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8b95b4-7f0b-41e5-9c0f-9b47c48bb8fe/OceanDNA-b23261.fa --refList OceanDNA-b23261/target_genomes.txt --output OceanDNA-b23261/fastani_result.tsv --threads 1
[2023-03-18 02:28:23,689] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:23,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:23,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:23,696] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:23,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:23,696] [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
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.783	56	1270	95	below_threshold
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	75.6789	56	1270	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.5843	74	1270	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.4809	60	1270	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.3213	75	1270	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.298	77	1270	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.2671	57	1270	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.1667	54	1270	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	75.0695	50	1270	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:23,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23261/tc_result.tsv
[2023-03-18 02:28:23,697] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:23,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:23,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference/checkm_data
[2023-03-18 02:28:23,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:23,756] [INFO] Task started: CheckM
[2023-03-18 02:28:23,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23261/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23261/checkm_input OceanDNA-b23261/checkm_result
[2023-03-18 02:29:23,744] [INFO] Task succeeded: CheckM
[2023-03-18 02:29:23,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:29:23,747] [INFO] ===== Completeness check finished =====
[2023-03-18 02:29:23,747] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:29:23,747] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23261/markers.fasta)
[2023-03-18 02:29:23,747] [INFO] Task started: Blastn
[2023-03-18 02:29:23,747] [INFO] Running command: blastn -query OceanDNA-b23261/markers.fasta -db /var/lib/cwl/stg2544bbb8-620a-4aca-9f8f-6158f7c1c471/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23261/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:29:24,823] [INFO] Task succeeded: Blastn
[2023-03-18 02:29:24,824] [INFO] Selected 25 target genomes.
[2023-03-18 02:29:24,824] [INFO] Target genome list was writen to OceanDNA-b23261/target_genomes_gtdb.txt
[2023-03-18 02:29:24,844] [INFO] Task started: fastANI
[2023-03-18 02:29:24,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8b95b4-7f0b-41e5-9c0f-9b47c48bb8fe/OceanDNA-b23261.fa --refList OceanDNA-b23261/target_genomes_gtdb.txt --output OceanDNA-b23261/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:42,790] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:42,794] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:42,794] [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_009649675.1	s__HT1-32 sp009649675	86.7099	1162	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__HT1-32;g__HT1-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	75.783	56	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	75.5843	74	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	75.298	77	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002195995.1	s__Inquilinus limosus_C	75.1619	58	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:42,794] [INFO] GTDB search result was written to OceanDNA-b23261/result_gtdb.tsv
[2023-03-18 02:29:42,794] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:42,795] [INFO] DFAST_QC result json was written to OceanDNA-b23261/dqc_result.json
[2023-03-18 02:29:42,795] [INFO] DFAST_QC completed!
[2023-03-18 02:29:42,795] [INFO] Total running time: 0h2m6s