[2023-06-17 16:58:56,306] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:58:56,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:58:56,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference
[2023-06-17 16:58:57,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:58:57,558] [INFO] Task started: Prodigal
[2023-06-17 16:58:57,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a1992c3-0bc5-4276-86e6-c08587d46334/GCA_009919205.1_ASM991920v1_genomic.fna.gz | prodigal -d GCA_009919205.1_ASM991920v1_genomic.fna/cds.fna -a GCA_009919205.1_ASM991920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:59:03,677] [INFO] Task succeeded: Prodigal
[2023-06-17 16:59:03,677] [INFO] Task started: HMMsearch
[2023-06-17 16:59:03,678] [INFO] Running command: hmmsearch --tblout GCA_009919205.1_ASM991920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference/reference_markers.hmm GCA_009919205.1_ASM991920v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:59:03,924] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:59:03,927] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3a1992c3-0bc5-4276-86e6-c08587d46334/GCA_009919205.1_ASM991920v1_genomic.fna.gz]
[2023-06-17 16:59:03,955] [INFO] Query marker FASTA was written to GCA_009919205.1_ASM991920v1_genomic.fna/markers.fasta
[2023-06-17 16:59:03,956] [INFO] Task started: Blastn
[2023-06-17 16:59:03,956] [INFO] Running command: blastn -query GCA_009919205.1_ASM991920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference/reference_markers.fasta -out GCA_009919205.1_ASM991920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:04,673] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:04,678] [INFO] Selected 14 target genomes.
[2023-06-17 16:59:04,678] [INFO] Target genome list was writen to GCA_009919205.1_ASM991920v1_genomic.fna/target_genomes.txt
[2023-06-17 16:59:04,682] [INFO] Task started: fastANI
[2023-06-17 16:59:04,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a1992c3-0bc5-4276-86e6-c08587d46334/GCA_009919205.1_ASM991920v1_genomic.fna.gz --refList GCA_009919205.1_ASM991920v1_genomic.fna/target_genomes.txt --output GCA_009919205.1_ASM991920v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:59:16,775] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:16,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:59:16,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:59:16,786] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:59:16,786] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:59:16,787] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.5123	152	403	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.3049	175	403	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.228	128	403	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.223	104	403	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.1164	98	403	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.7757	137	403	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.7631	93	403	95	below_threshold
Aeromicrobium marinum	strain=DSM 15272	GCA_000160775.2	219314	219314	type	True	76.2255	59	403	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	75.6818	84	403	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	75.6545	57	403	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	75.4741	102	403	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	75.4078	104	403	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:59:16,789] [INFO] DFAST Taxonomy check result was written to GCA_009919205.1_ASM991920v1_genomic.fna/tc_result.tsv
[2023-06-17 16:59:16,790] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:59:16,790] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:59:16,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference/checkm_data
[2023-06-17 16:59:16,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:59:16,832] [INFO] Task started: CheckM
[2023-06-17 16:59:16,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009919205.1_ASM991920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009919205.1_ASM991920v1_genomic.fna/checkm_input GCA_009919205.1_ASM991920v1_genomic.fna/checkm_result
[2023-06-17 16:59:41,973] [INFO] Task succeeded: CheckM
[2023-06-17 16:59:41,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:59:42,002] [INFO] ===== Completeness check finished =====
[2023-06-17 16:59:42,002] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:59:42,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009919205.1_ASM991920v1_genomic.fna/markers.fasta)
[2023-06-17 16:59:42,003] [INFO] Task started: Blastn
[2023-06-17 16:59:42,003] [INFO] Running command: blastn -query GCA_009919205.1_ASM991920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a878787-7d9c-4d65-8fa9-df40936cf81e/dqc_reference/reference_markers_gtdb.fasta -out GCA_009919205.1_ASM991920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:42,805] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:42,810] [INFO] Selected 14 target genomes.
[2023-06-17 16:59:42,810] [INFO] Target genome list was writen to GCA_009919205.1_ASM991920v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:59:42,817] [INFO] Task started: fastANI
[2023-06-17 16:59:42,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a1992c3-0bc5-4276-86e6-c08587d46334/GCA_009919205.1_ASM991920v1_genomic.fna.gz --refList GCA_009919205.1_ASM991920v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009919205.1_ASM991920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:59:49,358] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:49,375] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 16:59:49,375] [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
GCA_018969685.1	s__UBA3006 sp018969685	88.6245	337	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	78.5427	176	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013811855.1	s__JACCUL01 sp013811855	78.4727	126	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACCUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009927375.1	s__UBA3006 sp009927375	78.1027	72	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	78.1006	160	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.8672	138	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_007693335.1	s__SKSP01 sp007693335	77.694	139	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.5069	153	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.3839	147	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870865.1	s__F1-20-MAGs119 sp016870865	77.3502	88	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856375.1	s__UBA3006 sp017856375	77.3316	82	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009919275.1	s__F1-20-MAGs119 sp009919275	77.2932	66	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	99.53	99.53	0.87	0.87	2	-
GCA_010024485.1	s__Casp-actino5 sp010024485	76.9855	70	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.7236	96	403	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 16:59:49,377] [INFO] GTDB search result was written to GCA_009919205.1_ASM991920v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:59:49,378] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:59:49,384] [INFO] DFAST_QC result json was written to GCA_009919205.1_ASM991920v1_genomic.fna/dqc_result.json
[2023-06-17 16:59:49,384] [INFO] DFAST_QC completed!
[2023-06-17 16:59:49,384] [INFO] Total running time: 0h0m53s