[2024-01-24 13:32:34,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference
[2024-01-24 13:32:35,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:35,678] [INFO] Task started: Prodigal
[2024-01-24 13:32:35,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fb23171-5f9c-4c01-b2fa-27dd1e769916/GCF_900457435.1_43295_C02_genomic.fna.gz | prodigal -d GCF_900457435.1_43295_C02_genomic.fna/cds.fna -a GCF_900457435.1_43295_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:57,685] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:57,685] [INFO] Task started: HMMsearch
[2024-01-24 13:32:57,685] [INFO] Running command: hmmsearch --tblout GCF_900457435.1_43295_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference/reference_markers.hmm GCF_900457435.1_43295_C02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:58,112] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:58,113] [INFO] Found 6/6 markers.
[2024-01-24 13:32:58,166] [INFO] Query marker FASTA was written to GCF_900457435.1_43295_C02_genomic.fna/markers.fasta
[2024-01-24 13:32:58,167] [INFO] Task started: Blastn
[2024-01-24 13:32:58,167] [INFO] Running command: blastn -query GCF_900457435.1_43295_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference/reference_markers.fasta -out GCF_900457435.1_43295_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:58,800] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:58,803] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:58,804] [INFO] Target genome list was writen to GCF_900457435.1_43295_C02_genomic.fna/target_genomes.txt
[2024-01-24 13:32:58,812] [INFO] Task started: fastANI
[2024-01-24 13:32:58,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fb23171-5f9c-4c01-b2fa-27dd1e769916/GCF_900457435.1_43295_C02_genomic.fna.gz --refList GCF_900457435.1_43295_C02_genomic.fna/target_genomes.txt --output GCF_900457435.1_43295_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,088] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,101] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:11,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:11,102] [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
Sphingobacterium spiritivorum	strain=NCTC11386	GCA_900457435.1	258	258	suspected-type	True	100.0	1710	1712	95	conclusive
Sphingobacterium spiritivorum	strain=FDAARGOS_1144	GCA_016725645.1	258	258	suspected-type	True	99.9998	1710	1712	95	conclusive
Sphingobacterium spiritivorum	strain=ATCC 33861	GCA_000143765.1	258	258	suspected-type	True	99.9896	1693	1712	95	conclusive
Sphingobacterium phlebotomi	strain=SSI9	GCA_008180195.1	2605433	2605433	type	True	80.1323	135	1712	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_011046555.1	797291	797291	type	True	79.8784	148	1712	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_900107985.1	797291	797291	type	True	79.3055	143	1712	95	below_threshold
Sphingobacterium thalpophilum	strain=NCTC11429	GCA_901482695.1	259	259	type	True	78.557	180	1712	95	below_threshold
Sphingobacterium thalpophilum	strain=DSM 11723	GCA_000686625.1	259	259	type	True	78.1463	176	1712	95	below_threshold
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	78.0441	135	1712	95	below_threshold
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	78.0007	148	1712	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	77.9272	146	1712	95	below_threshold
Sphingobacterium griseoflavum	strain=CGMCC 1.12966	GCA_014653155.1	1474952	1474952	type	True	77.8548	102	1712	95	below_threshold
Sphingobacterium faecium	strain=DSM 11690	GCA_003054045.1	34087	34087	type	True	77.7013	181	1712	95	below_threshold
Sphingobacterium faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	77.5296	183	1712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,104] [INFO] DFAST Taxonomy check result was written to GCF_900457435.1_43295_C02_genomic.fna/tc_result.tsv
[2024-01-24 13:33:11,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:11,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:11,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference/checkm_data
[2024-01-24 13:33:11,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:11,153] [INFO] Task started: CheckM
[2024-01-24 13:33:11,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900457435.1_43295_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900457435.1_43295_C02_genomic.fna/checkm_input GCF_900457435.1_43295_C02_genomic.fna/checkm_result
[2024-01-24 13:34:13,669] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:13,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,692] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:13,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:13,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900457435.1_43295_C02_genomic.fna/markers.fasta)
[2024-01-24 13:34:13,694] [INFO] Task started: Blastn
[2024-01-24 13:34:13,694] [INFO] Running command: blastn -query GCF_900457435.1_43295_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd84f38a-bacc-458f-b9fe-87c764f038ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_900457435.1_43295_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:14,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:14,499] [INFO] Selected 13 target genomes.
[2024-01-24 13:34:14,499] [INFO] Target genome list was writen to GCF_900457435.1_43295_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:14,553] [INFO] Task started: fastANI
[2024-01-24 13:34:14,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fb23171-5f9c-4c01-b2fa-27dd1e769916/GCF_900457435.1_43295_C02_genomic.fna.gz --refList GCF_900457435.1_43295_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900457435.1_43295_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:26,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:26,476] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:26,476] [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_000143765.1	s__Sphingobacterium spiritivorum	99.9896	1693	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_016724845.1	s__Sphingobacterium spiritivorum_A	94.6264	1518	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.88	95.78	0.94	0.88	3	-
GCF_016725325.1	s__Sphingobacterium sp002418355	90.3903	1502	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.65	97.65	0.92	0.92	2	-
GCF_011046555.1	s__Sphingobacterium lactis	79.9959	144	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000783305.1	s__Sphingobacterium sp000783305	78.5388	357	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000245.1	s__Sphingobacterium sp002000245	78.2153	162	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500745.1	s__Sphingobacterium sp002500745	78.1294	173	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.61	98.61	0.89	0.89	2	-
GCF_006476045.1	s__Sphingobacterium lumbrici	78.0864	134	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015210005.1	s__Sphingobacterium sp015210005	77.9191	129	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653155.1	s__Sphingobacterium griseoflavum	77.8123	104	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012030425.1	s__Sphingobacterium kitahiroshimense	77.5463	208	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.48	96.84	0.85	0.82	6	-
GCF_011043525.1	s__Sphingobacterium sp011043525	77.0168	111	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100435.1	s__Pedobacter sp900100435	75.8404	53	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:26,478] [INFO] GTDB search result was written to GCF_900457435.1_43295_C02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:26,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:26,482] [INFO] DFAST_QC result json was written to GCF_900457435.1_43295_C02_genomic.fna/dqc_result.json
[2024-01-24 13:34:26,482] [INFO] DFAST_QC completed!
[2024-01-24 13:34:26,482] [INFO] Total running time: 0h1m52s