[2024-01-25 19:35:05,731] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:05,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:05,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference
[2024-01-25 19:35:06,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:06,901] [INFO] Task started: Prodigal
[2024-01-25 19:35:06,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bf07a1c-22c2-4043-910e-3a18147a1295/GCF_002157875.1_ASM215787v1_genomic.fna.gz | prodigal -d GCF_002157875.1_ASM215787v1_genomic.fna/cds.fna -a GCF_002157875.1_ASM215787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:12,609] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:12,609] [INFO] Task started: HMMsearch
[2024-01-25 19:35:12,609] [INFO] Running command: hmmsearch --tblout GCF_002157875.1_ASM215787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference/reference_markers.hmm GCF_002157875.1_ASM215787v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:12,838] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:12,840] [INFO] Found 6/6 markers.
[2024-01-25 19:35:12,865] [INFO] Query marker FASTA was written to GCF_002157875.1_ASM215787v1_genomic.fna/markers.fasta
[2024-01-25 19:35:12,865] [INFO] Task started: Blastn
[2024-01-25 19:35:12,865] [INFO] Running command: blastn -query GCF_002157875.1_ASM215787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference/reference_markers.fasta -out GCF_002157875.1_ASM215787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:13,569] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:13,572] [INFO] Selected 22 target genomes.
[2024-01-25 19:35:13,573] [INFO] Target genome list was writen to GCF_002157875.1_ASM215787v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:13,595] [INFO] Task started: fastANI
[2024-01-25 19:35:13,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf07a1c-22c2-4043-910e-3a18147a1295/GCF_002157875.1_ASM215787v1_genomic.fna.gz --refList GCF_002157875.1_ASM215787v1_genomic.fna/target_genomes.txt --output GCF_002157875.1_ASM215787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:27,148] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:27,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:27,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:27,156] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:27,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:27,156] [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
Oceanisphaera avium	strain=AMac2203	GCA_002157875.1	1903694	1903694	type	True	100.0	967	967	95	conclusive
Oceanisphaera profunda	strain=SM1222	GCA_002157895.1	1416627	1416627	type	True	80.6375	561	967	95	below_threshold
Oceanisphaera pacifica	strain=DM8	GCA_017498065.1	2818389	2818389	type	True	79.1058	386	967	95	below_threshold
Oceanisphaera marina	strain=CGMCC 1.15923	GCA_014643915.1	2017550	2017550	type	True	78.7437	305	967	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	78.4429	183	967	95	below_threshold
Agarivorans litoreus	strain=NBRC 110444	GCA_019649015.1	1510455	1510455	type	True	78.3763	55	967	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	77.9496	114	967	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	77.6067	113	967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:27,158] [INFO] DFAST Taxonomy check result was written to GCF_002157875.1_ASM215787v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:27,158] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:27,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:27,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference/checkm_data
[2024-01-25 19:35:27,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:27,188] [INFO] Task started: CheckM
[2024-01-25 19:35:27,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002157875.1_ASM215787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002157875.1_ASM215787v1_genomic.fna/checkm_input GCF_002157875.1_ASM215787v1_genomic.fna/checkm_result
[2024-01-25 19:35:48,667] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:48,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:48,692] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:48,693] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:48,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002157875.1_ASM215787v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:48,693] [INFO] Task started: Blastn
[2024-01-25 19:35:48,693] [INFO] Running command: blastn -query GCF_002157875.1_ASM215787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a33ed35-88f3-422d-83a9-e6d4d27c589e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002157875.1_ASM215787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:49,835] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:49,842] [INFO] Selected 16 target genomes.
[2024-01-25 19:35:49,842] [INFO] Target genome list was writen to GCF_002157875.1_ASM215787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:49,858] [INFO] Task started: fastANI
[2024-01-25 19:35:49,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf07a1c-22c2-4043-910e-3a18147a1295/GCF_002157875.1_ASM215787v1_genomic.fna.gz --refList GCF_002157875.1_ASM215787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002157875.1_ASM215787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:01,090] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:01,096] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:01,096] [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
GCF_002157875.1	s__Oceanisphaera avium	100.0	967	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002157895.1	s__Oceanisphaera profunda	80.6051	560	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883865.1	s__Oceanisphaera merdipullorum	79.9128	449	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498065.1	s__Oceanisphaera sp017498065	79.0861	389	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643915.1	s__Oceanisphaera marina	78.7931	302	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518835.1	s__Oceanisphaera sp012518835	78.1886	284	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012775.1	s__Zobellella_C endophytica	77.9496	114	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:01,097] [INFO] GTDB search result was written to GCF_002157875.1_ASM215787v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:01,098] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:01,102] [INFO] DFAST_QC result json was written to GCF_002157875.1_ASM215787v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:01,102] [INFO] DFAST_QC completed!
[2024-01-25 19:36:01,102] [INFO] Total running time: 0h0m55s