[2024-01-24 12:13:59,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:59,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:59,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference
[2024-01-24 12:14:00,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,665] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg91854a9c-16f6-4ede-b2f7-035fe72e39e0/GCF_000511175.1_ASM51117v1_genomic.fna.gz | prodigal -d GCF_000511175.1_ASM51117v1_genomic.fna/cds.fna -a GCF_000511175.1_ASM51117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:14,849] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:14,850] [INFO] Task started: HMMsearch
[2024-01-24 12:14:14,850] [INFO] Running command: hmmsearch --tblout GCF_000511175.1_ASM51117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference/reference_markers.hmm GCF_000511175.1_ASM51117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:15,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:15,221] [INFO] Found 6/6 markers.
[2024-01-24 12:14:15,252] [INFO] Query marker FASTA was written to GCF_000511175.1_ASM51117v1_genomic.fna/markers.fasta
[2024-01-24 12:14:15,252] [INFO] Task started: Blastn
[2024-01-24 12:14:15,252] [INFO] Running command: blastn -query GCF_000511175.1_ASM51117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference/reference_markers.fasta -out GCF_000511175.1_ASM51117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:15,928] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:15,932] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:15,932] [INFO] Target genome list was writen to GCF_000511175.1_ASM51117v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:15,943] [INFO] Task started: fastANI
[2024-01-24 12:14:15,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg91854a9c-16f6-4ede-b2f7-035fe72e39e0/GCF_000511175.1_ASM51117v1_genomic.fna.gz --refList GCF_000511175.1_ASM51117v1_genomic.fna/target_genomes.txt --output GCF_000511175.1_ASM51117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:32,133] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:32,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:32,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:32,146] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:32,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:32,147] [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
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	99.9993	1075	1082	95	conclusive
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	77.191	172	1082	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.9605	112	1082	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	76.8975	110	1082	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.7629	90	1082	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.6612	60	1082	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.5165	88	1082	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.3663	79	1082	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.3392	79	1082	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	76.3148	56	1082	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.2832	54	1082	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.2625	97	1082	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.2012	87	1082	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.1284	91	1082	95	below_threshold
Agriterribacter humi	strain=YJ03	GCA_009192765.1	1104781	1104781	type	True	75.8969	52	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:32,149] [INFO] DFAST Taxonomy check result was written to GCF_000511175.1_ASM51117v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:32,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:32,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:32,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference/checkm_data
[2024-01-24 12:14:32,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:32,185] [INFO] Task started: CheckM
[2024-01-24 12:14:32,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000511175.1_ASM51117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000511175.1_ASM51117v1_genomic.fna/checkm_input GCF_000511175.1_ASM51117v1_genomic.fna/checkm_result
[2024-01-24 12:15:17,088] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:17,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.47%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:17,115] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:17,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:17,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000511175.1_ASM51117v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:17,117] [INFO] Task started: Blastn
[2024-01-24 12:15:17,117] [INFO] Running command: blastn -query GCF_000511175.1_ASM51117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg817ad7d6-5f82-412a-aa9e-ed5f80a2e4eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000511175.1_ASM51117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:18,142] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:18,147] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:18,147] [INFO] Target genome list was writen to GCF_000511175.1_ASM51117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:18,233] [INFO] Task started: fastANI
[2024-01-24 12:15:18,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg91854a9c-16f6-4ede-b2f7-035fe72e39e0/GCF_000511175.1_ASM51117v1_genomic.fna.gz --refList GCF_000511175.1_ASM51117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000511175.1_ASM51117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:23,411] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:23,418] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:23,419] [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_000511175.1	s__Sediminibacterium salmoneum	99.9993	1075	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000508085.1	s__Sediminibacterium sp000508085	89.6733	918	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281875.1	s__Sediminibacterium sp002281875	80.2673	506	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.93	99.91	0.97	0.97	3	-
GCA_002281575.1	s__Sediminibacterium sp002281575	80.0121	538	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017996795.1	s__Sediminibacterium sp017996795	79.768	347	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829005.1	s__Sediminibacterium sp001829005	79.7633	540	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.07	96.16	0.93	0.87	3	-
GCA_002786355.1	s__Sediminibacterium sp002786355	79.6885	492	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.29	98.29	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,420] [INFO] GTDB search result was written to GCF_000511175.1_ASM51117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:23,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:23,424] [INFO] DFAST_QC result json was written to GCF_000511175.1_ASM51117v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:23,424] [INFO] DFAST_QC completed!
[2024-01-24 12:15:23,424] [INFO] Total running time: 0h1m24s