[2024-01-24 12:05:26,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,621] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference
[2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,677] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4e00c9b-a26c-4db6-9503-0e0a331a4104/GCF_016595415.1_ASM1659541v1_genomic.fna.gz | prodigal -d GCF_016595415.1_ASM1659541v1_genomic.fna/cds.fna -a GCF_016595415.1_ASM1659541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:57,308] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:57,308] [INFO] Task started: HMMsearch
[2024-01-24 12:05:57,308] [INFO] Running command: hmmsearch --tblout GCF_016595415.1_ASM1659541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference/reference_markers.hmm GCF_016595415.1_ASM1659541v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:57,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:57,607] [INFO] Found 6/6 markers.
[2024-01-24 12:05:57,643] [INFO] Query marker FASTA was written to GCF_016595415.1_ASM1659541v1_genomic.fna/markers.fasta
[2024-01-24 12:05:57,644] [INFO] Task started: Blastn
[2024-01-24 12:05:57,644] [INFO] Running command: blastn -query GCF_016595415.1_ASM1659541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference/reference_markers.fasta -out GCF_016595415.1_ASM1659541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:58,249] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:58,253] [INFO] Selected 15 target genomes.
[2024-01-24 12:05:58,253] [INFO] Target genome list was writen to GCF_016595415.1_ASM1659541v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:58,261] [INFO] Task started: fastANI
[2024-01-24 12:05:58,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e00c9b-a26c-4db6-9503-0e0a331a4104/GCF_016595415.1_ASM1659541v1_genomic.fna.gz --refList GCF_016595415.1_ASM1659541v1_genomic.fna/target_genomes.txt --output GCF_016595415.1_ASM1659541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:09,776] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:09,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:09,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:09,789] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:09,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:09,790] [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
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	100.0	1310	1314	95	conclusive
Roseibacillus persicicus	strain=KCTC 12988	GCA_014651675.1	454148	454148	type	True	78.0048	364	1314	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.9168	93	1314	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.5797	86	1314	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	76.5243	73	1314	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.2192	55	1314	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.1568	67	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:09,791] [INFO] DFAST Taxonomy check result was written to GCF_016595415.1_ASM1659541v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:09,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:09,792] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:09,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference/checkm_data
[2024-01-24 12:06:09,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:09,841] [INFO] Task started: CheckM
[2024-01-24 12:06:09,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595415.1_ASM1659541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595415.1_ASM1659541v1_genomic.fna/checkm_input GCF_016595415.1_ASM1659541v1_genomic.fna/checkm_result
[2024-01-24 12:07:20,095] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:20,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:20,122] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:20,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:20,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595415.1_ASM1659541v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:20,123] [INFO] Task started: Blastn
[2024-01-24 12:07:20,123] [INFO] Running command: blastn -query GCF_016595415.1_ASM1659541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fb7197b-7242-4a78-b3ca-37e345eeffa5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595415.1_ASM1659541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:21,017] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:21,021] [INFO] Selected 25 target genomes.
[2024-01-24 12:07:21,022] [INFO] Target genome list was writen to GCF_016595415.1_ASM1659541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:21,046] [INFO] Task started: fastANI
[2024-01-24 12:07:21,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e00c9b-a26c-4db6-9503-0e0a331a4104/GCF_016595415.1_ASM1659541v1_genomic.fna.gz --refList GCF_016595415.1_ASM1659541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595415.1_ASM1659541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:37,120] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:37,134] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:37,134] [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_016595415.1	s__Roseibacillus ishigakijimensis	100.0	1310	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014651675.1	s__Roseibacillus persicicus	78.0141	363	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	76.9168	93	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	76.8334	103	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	76.6743	82	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016811075.1	s__UBA985 sp016811075	76.6473	76	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCA_003820635.1	s__Luteolibacter sp003820635	76.6468	59	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182405.1	s__SW10 sp905182405	76.5768	54	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402445.1	s__Luteolibacter sp018402445	76.4932	67	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	76.4078	98	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.3863	92	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713245.1	s__Prosthecobacter sp016713245	76.3413	54	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344525.1	s__Arctic95D-9 sp002344525	76.1546	72	1314	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:37,136] [INFO] GTDB search result was written to GCF_016595415.1_ASM1659541v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:37,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:37,142] [INFO] DFAST_QC result json was written to GCF_016595415.1_ASM1659541v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:37,143] [INFO] DFAST_QC completed!
[2024-01-24 12:07:37,143] [INFO] Total running time: 0h2m11s