[2024-01-24 13:31:26,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:26,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:26,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference
[2024-01-24 13:31:27,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:27,462] [INFO] Task started: Prodigal
[2024-01-24 13:31:27,462] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9e11507-5b41-4f91-a5b8-3b0f8c46b54a/GCF_003991355.1_ASM399135v1_genomic.fna.gz | prodigal -d GCF_003991355.1_ASM399135v1_genomic.fna/cds.fna -a GCF_003991355.1_ASM399135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:03,666] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:03,667] [INFO] Task started: HMMsearch
[2024-01-24 13:32:03,667] [INFO] Running command: hmmsearch --tblout GCF_003991355.1_ASM399135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference/reference_markers.hmm GCF_003991355.1_ASM399135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:04,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:04,003] [INFO] Found 6/6 markers.
[2024-01-24 13:32:04,058] [INFO] Query marker FASTA was written to GCF_003991355.1_ASM399135v1_genomic.fna/markers.fasta
[2024-01-24 13:32:04,059] [INFO] Task started: Blastn
[2024-01-24 13:32:04,059] [INFO] Running command: blastn -query GCF_003991355.1_ASM399135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference/reference_markers.fasta -out GCF_003991355.1_ASM399135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:04,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:04,659] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:04,660] [INFO] Target genome list was writen to GCF_003991355.1_ASM399135v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:04,841] [INFO] Task started: fastANI
[2024-01-24 13:32:04,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9e11507-5b41-4f91-a5b8-3b0f8c46b54a/GCF_003991355.1_ASM399135v1_genomic.fna.gz --refList GCF_003991355.1_ASM399135v1_genomic.fna/target_genomes.txt --output GCF_003991355.1_ASM399135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:23,299] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:23,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:23,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:23,312] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:23,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:23,313] [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
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	89.207	1855	2217	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	89.1692	1861	2217	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	76.9699	322	2217	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.898	316	2217	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	76.684	206	2217	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.5595	252	2217	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.4983	228	2217	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.4749	84	2217	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	76.4287	201	2217	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.3903	231	2217	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.2934	90	2217	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	76.0819	91	2217	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.9127	73	2217	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	75.8366	114	2217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:23,315] [INFO] DFAST Taxonomy check result was written to GCF_003991355.1_ASM399135v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:23,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:23,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:23,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference/checkm_data
[2024-01-24 13:32:23,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:23,383] [INFO] Task started: CheckM
[2024-01-24 13:32:23,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003991355.1_ASM399135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003991355.1_ASM399135v1_genomic.fna/checkm_input GCF_003991355.1_ASM399135v1_genomic.fna/checkm_result
[2024-01-24 13:34:02,907] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:02,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:02,933] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:02,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:02,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003991355.1_ASM399135v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:02,934] [INFO] Task started: Blastn
[2024-01-24 13:34:02,934] [INFO] Running command: blastn -query GCF_003991355.1_ASM399135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0874dd4c-15da-4809-9bba-56afa05fb94e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003991355.1_ASM399135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:03,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:03,997] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:03,997] [INFO] Target genome list was writen to GCF_003991355.1_ASM399135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:04,167] [INFO] Task started: fastANI
[2024-01-24 13:34:04,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9e11507-5b41-4f91-a5b8-3b0f8c46b54a/GCF_003991355.1_ASM399135v1_genomic.fna.gz --refList GCF_003991355.1_ASM399135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003991355.1_ASM399135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:18,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:18,766] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:18,767] [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_003991355.1	s__Pseudobacter rhizosphaerae	100.0	2215	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	89.2065	1854	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744805.1	s__Pseudobacter sp017744805	82.4293	1039	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927185.1	s__Pseudobacter sp012927185	80.2268	891	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849455.1	s__Pseudobacter sp017849455	77.7562	485	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003555545.1	s__Paraflavitalea soli	76.9616	323	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759375.1	s__Paraflavitalea devenefica	76.913	314	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	76.5834	249	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	76.3983	230	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001898405.1	s__46-32 sp001898405	76.2831	155	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
GCF_003568665.1	s__Chitinophaga alhagiae	76.0819	91	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:18,769] [INFO] GTDB search result was written to GCF_003991355.1_ASM399135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:18,770] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:18,774] [INFO] DFAST_QC result json was written to GCF_003991355.1_ASM399135v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:18,774] [INFO] DFAST_QC completed!
[2024-01-24 13:34:18,774] [INFO] Total running time: 0h2m53s