[2024-01-25 18:10:35,869] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference
[2024-01-25 18:10:37,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:37,082] [INFO] Task started: Prodigal
[2024-01-25 18:10:37,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg29377276-a1b6-425f-a86b-31b56a170818/GCF_016901055.1_ASM1690105v1_genomic.fna.gz | prodigal -d GCF_016901055.1_ASM1690105v1_genomic.fna/cds.fna -a GCF_016901055.1_ASM1690105v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:45,885] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:45,886] [INFO] Task started: HMMsearch
[2024-01-25 18:10:45,886] [INFO] Running command: hmmsearch --tblout GCF_016901055.1_ASM1690105v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference/reference_markers.hmm GCF_016901055.1_ASM1690105v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:46,118] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:46,119] [INFO] Found 6/6 markers.
[2024-01-25 18:10:46,157] [INFO] Query marker FASTA was written to GCF_016901055.1_ASM1690105v1_genomic.fna/markers.fasta
[2024-01-25 18:10:46,157] [INFO] Task started: Blastn
[2024-01-25 18:10:46,157] [INFO] Running command: blastn -query GCF_016901055.1_ASM1690105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference/reference_markers.fasta -out GCF_016901055.1_ASM1690105v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:46,704] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:46,707] [INFO] Selected 16 target genomes.
[2024-01-25 18:10:46,708] [INFO] Target genome list was writen to GCF_016901055.1_ASM1690105v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:46,713] [INFO] Task started: fastANI
[2024-01-25 18:10:46,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg29377276-a1b6-425f-a86b-31b56a170818/GCF_016901055.1_ASM1690105v1_genomic.fna.gz --refList GCF_016901055.1_ASM1690105v1_genomic.fna/target_genomes.txt --output GCF_016901055.1_ASM1690105v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:59,513] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:59,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:59,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:59,520] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:10:59,520] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:10:59,520] [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
Alteribacter salitolerans	strain=APA H-16(1)	GCA_016901055.1	2912333	2912333	type	True	100.0	1381	1382	95	inconclusive
Alteribacter keqinensis	strain=KQ-3	GCA_003710255.1	2483800	2483800	type	True	98.0446	1315	1382	95	inconclusive
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	80.1386	631	1382	95	below_threshold
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	78.6309	303	1382	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	78.235	286	1382	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	77.2503	98	1382	95	below_threshold
Alkalicoccus halolimnae	strain=BZ-SZ-XJ29	GCA_008014775.1	1667239	1667239	type	True	77.1342	55	1382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:59,521] [INFO] DFAST Taxonomy check result was written to GCF_016901055.1_ASM1690105v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:59,522] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:59,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:59,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference/checkm_data
[2024-01-25 18:10:59,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:59,564] [INFO] Task started: CheckM
[2024-01-25 18:10:59,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016901055.1_ASM1690105v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016901055.1_ASM1690105v1_genomic.fna/checkm_input GCF_016901055.1_ASM1690105v1_genomic.fna/checkm_result
[2024-01-25 18:11:29,411] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:29,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:29,431] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:29,432] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:29,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016901055.1_ASM1690105v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:29,432] [INFO] Task started: Blastn
[2024-01-25 18:11:29,432] [INFO] Running command: blastn -query GCF_016901055.1_ASM1690105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b48252-0cb2-4916-a06d-9d9355e1d7a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016901055.1_ASM1690105v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:30,208] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:30,211] [INFO] Selected 21 target genomes.
[2024-01-25 18:11:30,211] [INFO] Target genome list was writen to GCF_016901055.1_ASM1690105v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:30,229] [INFO] Task started: fastANI
[2024-01-25 18:11:30,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg29377276-a1b6-425f-a86b-31b56a170818/GCF_016901055.1_ASM1690105v1_genomic.fna.gz --refList GCF_016901055.1_ASM1690105v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016901055.1_ASM1690105v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:45,753] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:45,759] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:45,759] [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_003710255.1	s__Alteribacter sp003710255	98.0446	1315	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	98.04	98.04	0.95	0.95	2	conclusive
GCF_000429705.1	s__Alteribacter aurantiacus	80.1421	631	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002352765.1	s__Alteribacter populi	78.6601	259	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	-
GCF_003226345.1	s__Alteribacter lacisalsi	78.6044	305	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006007885.1	s__Alteribacter natronophilus	78.2429	286	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107275.1	s__Evansella caseinilytica	77.5473	66	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014775.1	s__Alkalicoccus halolimnae	77.1342	55	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692495.1	s__Alkalicoccus sp007692495	76.7139	50	1382	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:45,760] [INFO] GTDB search result was written to GCF_016901055.1_ASM1690105v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:45,761] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:45,763] [INFO] DFAST_QC result json was written to GCF_016901055.1_ASM1690105v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:45,764] [INFO] DFAST_QC completed!
[2024-01-25 18:11:45,764] [INFO] Total running time: 0h1m10s