[2024-01-24 13:37:28,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:28,069] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:28,069] [INFO] DQC Reference Directory: /var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference
[2024-01-24 13:37:29,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,306] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,306] [INFO] Running command: gunzip -c /var/lib/cwl/stgf759028e-bbbc-4a39-be44-c7c94d0d99d2/GCF_000416985.1_23.k55_genomic.fna.gz | prodigal -d GCF_000416985.1_23.k55_genomic.fna/cds.fna -a GCF_000416985.1_23.k55_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:51,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:51,655] [INFO] Task started: HMMsearch
[2024-01-24 13:37:51,655] [INFO] Running command: hmmsearch --tblout GCF_000416985.1_23.k55_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference/reference_markers.hmm GCF_000416985.1_23.k55_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:51,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:51,973] [INFO] Found 6/6 markers.
[2024-01-24 13:37:52,018] [INFO] Query marker FASTA was written to GCF_000416985.1_23.k55_genomic.fna/markers.fasta
[2024-01-24 13:37:52,018] [INFO] Task started: Blastn
[2024-01-24 13:37:52,018] [INFO] Running command: blastn -query GCF_000416985.1_23.k55_genomic.fna/markers.fasta -db /var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference/reference_markers.fasta -out GCF_000416985.1_23.k55_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:52,644] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:52,648] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:52,648] [INFO] Target genome list was writen to GCF_000416985.1_23.k55_genomic.fna/target_genomes.txt
[2024-01-24 13:37:52,790] [INFO] Task started: fastANI
[2024-01-24 13:37:52,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgf759028e-bbbc-4a39-be44-c7c94d0d99d2/GCF_000416985.1_23.k55_genomic.fna.gz --refList GCF_000416985.1_23.k55_genomic.fna/target_genomes.txt --output GCF_000416985.1_23.k55_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:05,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:05,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:05,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:05,083] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:05,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:05,084] [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 paucimobilis	strain=HER1398	GCA_000416985.1	1385985	1385985	type	True	100.0	1671	1697	95	conclusive
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	89.6007	1073	1697	95	below_threshold
Sphingobacterium tabacisoli	strain=h337	GCA_017908035.1	2044855	2044855	type	True	86.5194	980	1697	95	below_threshold
Sphingobacterium yanglingense	strain=DSM 28353	GCA_004363245.1	1437280	1437280	type	True	83.0676	874	1697	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	80.254	625	1697	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	78.256	135	1697	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	78.1517	194	1697	95	below_threshold
Sphingobacterium spiritivorum	strain=ATCC 33861	GCA_000143765.1	258	258	suspected-type	True	78.1386	126	1697	95	below_threshold
Sphingobacterium psychroaquaticum	strain=DSM 22418	GCA_900177625.1	561061	561061	type	True	77.7511	139	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:05,086] [INFO] DFAST Taxonomy check result was written to GCF_000416985.1_23.k55_genomic.fna/tc_result.tsv
[2024-01-24 13:38:05,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:05,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:05,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference/checkm_data
[2024-01-24 13:38:05,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:05,139] [INFO] Task started: CheckM
[2024-01-24 13:38:05,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000416985.1_23.k55_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000416985.1_23.k55_genomic.fna/checkm_input GCF_000416985.1_23.k55_genomic.fna/checkm_result
[2024-01-24 13:39:08,248] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:08,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:08,270] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:08,270] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:08,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000416985.1_23.k55_genomic.fna/markers.fasta)
[2024-01-24 13:39:08,271] [INFO] Task started: Blastn
[2024-01-24 13:39:08,271] [INFO] Running command: blastn -query GCF_000416985.1_23.k55_genomic.fna/markers.fasta -db /var/lib/cwl/stgbec898ab-598f-45d4-a0b4-8970f1c36635/dqc_reference/reference_markers_gtdb.fasta -out GCF_000416985.1_23.k55_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:09,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:09,101] [INFO] Selected 15 target genomes.
[2024-01-24 13:39:09,101] [INFO] Target genome list was writen to GCF_000416985.1_23.k55_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:09,409] [INFO] Task started: fastANI
[2024-01-24 13:39:09,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgf759028e-bbbc-4a39-be44-c7c94d0d99d2/GCF_000416985.1_23.k55_genomic.fna.gz --refList GCF_000416985.1_23.k55_genomic.fna/target_genomes_gtdb.txt --output GCF_000416985.1_23.k55_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:22,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:22,291] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:22,291] [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_000416985.1	s__Sphingobacterium paucimobilis	100.0	1656	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016746095.1	s__Sphingobacterium sp016746095	89.6019	1074	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017908035.1	s__Sphingobacterium tabacisoli	86.5551	978	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363245.1	s__Sphingobacterium yanglingense	83.0438	877	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011007365.1	s__Sphingobacterium sp011007365	80.9037	573	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.58	99.33	0.95	0.93	4	-
GCF_900168125.1	s__Sphingobacterium nematocida	80.2368	627	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209965.1	s__Sphingobacterium sp015209965	78.4988	153	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002322865.1	s__Sphingobacterium sp002322865	78.4469	116	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	78.3906	133	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_003076635.1	s__Sphingobacterium sp003076635	77.8456	94	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177625.1	s__Sphingobacterium psychroaquaticum	77.7913	139	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.08	99.08	0.93	0.93	2	-
GCF_002980575.1	s__Sphingobacterium gobiense	77.2028	110	1697	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:22,293] [INFO] GTDB search result was written to GCF_000416985.1_23.k55_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:22,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:22,297] [INFO] DFAST_QC result json was written to GCF_000416985.1_23.k55_genomic.fna/dqc_result.json
[2024-01-24 13:39:22,297] [INFO] DFAST_QC completed!
[2024-01-24 13:39:22,297] [INFO] Total running time: 0h1m54s