[2024-01-24 12:06:18,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:18,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:18,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference
[2024-01-24 12:06:20,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:20,131] [INFO] Task started: Prodigal
[2024-01-24 12:06:20,131] [INFO] Running command: gunzip -c /var/lib/cwl/stgd87747a7-0394-4399-8ad0-ad1eb7133a4c/GCF_030409555.1_ASM3040955v1_genomic.fna.gz | prodigal -d GCF_030409555.1_ASM3040955v1_genomic.fna/cds.fna -a GCF_030409555.1_ASM3040955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:35,504] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:35,505] [INFO] Task started: HMMsearch
[2024-01-24 12:06:35,505] [INFO] Running command: hmmsearch --tblout GCF_030409555.1_ASM3040955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference/reference_markers.hmm GCF_030409555.1_ASM3040955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:35,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:35,828] [INFO] Found 6/6 markers.
[2024-01-24 12:06:35,873] [INFO] Query marker FASTA was written to GCF_030409555.1_ASM3040955v1_genomic.fna/markers.fasta
[2024-01-24 12:06:35,873] [INFO] Task started: Blastn
[2024-01-24 12:06:35,874] [INFO] Running command: blastn -query GCF_030409555.1_ASM3040955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference/reference_markers.fasta -out GCF_030409555.1_ASM3040955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:36,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:36,827] [INFO] Selected 23 target genomes.
[2024-01-24 12:06:36,827] [INFO] Target genome list was writen to GCF_030409555.1_ASM3040955v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:36,838] [INFO] Task started: fastANI
[2024-01-24 12:06:36,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgd87747a7-0394-4399-8ad0-ad1eb7133a4c/GCF_030409555.1_ASM3040955v1_genomic.fna.gz --refList GCF_030409555.1_ASM3040955v1_genomic.fna/target_genomes.txt --output GCF_030409555.1_ASM3040955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:56,696] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:56,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:56,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:56,721] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:56,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:56,721] [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
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	79.8304	602	1521	95	below_threshold
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	79.6304	618	1521	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	79.4362	648	1521	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.6824	261	1521	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	77.5121	210	1521	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	77.5096	254	1521	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	77.4947	225	1521	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	77.4822	233	1521	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	77.4598	216	1521	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	77.3671	183	1521	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	77.2937	186	1521	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	77.2385	183	1521	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	77.2097	220	1521	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	77.1499	177	1521	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	77.1079	227	1521	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	77.1019	170	1521	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	77.0013	126	1521	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.4919	149	1521	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.4639	150	1521	95	below_threshold
Paraburkholderia piptadeniae	strain=STM 7183	GCA_900007165.2	1701573	1701573	type	True	76.2766	72	1521	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.2629	148	1521	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.0151	122	1521	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	75.7233	76	1521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:56,723] [INFO] DFAST Taxonomy check result was written to GCF_030409555.1_ASM3040955v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:56,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:56,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:56,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference/checkm_data
[2024-01-24 12:06:56,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:56,772] [INFO] Task started: CheckM
[2024-01-24 12:06:56,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409555.1_ASM3040955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409555.1_ASM3040955v1_genomic.fna/checkm_input GCF_030409555.1_ASM3040955v1_genomic.fna/checkm_result
[2024-01-24 12:07:42,464] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:42,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:42,492] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:42,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:42,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409555.1_ASM3040955v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:42,493] [INFO] Task started: Blastn
[2024-01-24 12:07:42,494] [INFO] Running command: blastn -query GCF_030409555.1_ASM3040955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85cb9b9-1a04-4391-9bc5-4357deac7985/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409555.1_ASM3040955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:44,088] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:44,091] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:44,092] [INFO] Target genome list was writen to GCF_030409555.1_ASM3040955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:44,103] [INFO] Task started: fastANI
[2024-01-24 12:07:44,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgd87747a7-0394-4399-8ad0-ad1eb7133a4c/GCF_030409555.1_ASM3040955v1_genomic.fna.gz --refList GCF_030409555.1_ASM3040955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409555.1_ASM3040955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:56,191] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:56,209] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:56,209] [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_900119825.1	s__Chitinimonas taiwanensis	79.8121	605	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	96.92	96.91	0.93	0.93	3	-
GCF_007431345.1	s__Chitinimonas arctica	79.6175	619	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428465.1	s__Chitinimonas koreensis	79.4322	649	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234745.1	s__JAFAKZ01 sp019234745	78.3136	290	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__JAFAKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002735695.1	s__Chitinimonas sp002735695	78.2049	294	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCA_019084025.1	s__DAT-1 sp019084025	78.0425	199	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__DAT-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	77.5096	254	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	77.5009	234	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008275125.1	s__Chromobacterium paludis	77.4696	234	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808185.1	s__Jeongeupia sp001808185	77.268	186	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865585.1	s__Jeongeupia naejangsanensis	77.2533	182	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641365.1	s__Leeia aquatica	77.1499	177	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260425.1	s__Paludibacterium sp018260425	77.0564	106	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115065.1	s__Formivibrio citricus	77.0013	126	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002340095.1	s__Azovibrio sp002340095	76.7637	106	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000471925.1	s__Cupriavidus pickettii_A	76.4489	179	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,211] [INFO] GTDB search result was written to GCF_030409555.1_ASM3040955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:56,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:56,216] [INFO] DFAST_QC result json was written to GCF_030409555.1_ASM3040955v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:56,216] [INFO] DFAST_QC completed!
[2024-01-24 12:07:56,216] [INFO] Total running time: 0h1m37s