[2023-06-18 13:03:39,700] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:39,702] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:39,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference
[2023-06-18 13:03:42,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:42,181] [INFO] Task started: Prodigal
[2023-06-18 13:03:42,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg80cf4569-83b4-4116-b696-7272dda58ee4/GCA_013697265.1_ASM1369726v1_genomic.fna.gz | prodigal -d GCA_013697265.1_ASM1369726v1_genomic.fna/cds.fna -a GCA_013697265.1_ASM1369726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:48,935] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:48,936] [INFO] Task started: HMMsearch
[2023-06-18 13:03:48,936] [INFO] Running command: hmmsearch --tblout GCA_013697265.1_ASM1369726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference/reference_markers.hmm GCA_013697265.1_ASM1369726v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:49,120] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:49,121] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg80cf4569-83b4-4116-b696-7272dda58ee4/GCA_013697265.1_ASM1369726v1_genomic.fna.gz]
[2023-06-18 13:03:49,154] [INFO] Query marker FASTA was written to GCA_013697265.1_ASM1369726v1_genomic.fna/markers.fasta
[2023-06-18 13:03:49,154] [INFO] Task started: Blastn
[2023-06-18 13:03:49,154] [INFO] Running command: blastn -query GCA_013697265.1_ASM1369726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference/reference_markers.fasta -out GCA_013697265.1_ASM1369726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:49,831] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:49,837] [INFO] Selected 22 target genomes.
[2023-06-18 13:03:49,837] [INFO] Target genome list was writen to GCA_013697265.1_ASM1369726v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:49,843] [INFO] Task started: fastANI
[2023-06-18 13:03:49,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cf4569-83b4-4116-b696-7272dda58ee4/GCA_013697265.1_ASM1369726v1_genomic.fna.gz --refList GCA_013697265.1_ASM1369726v1_genomic.fna/target_genomes.txt --output GCA_013697265.1_ASM1369726v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:04:06,068] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:06,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:04:06,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:04:06,082] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:04:06,082] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 13:04:06,082] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.1564	94	618	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.0815	109	618	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.9389	69	618	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.8308	74	618	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.7194	64	618	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6186	89	618	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.5766	101	618	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	75.0629	68	618	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	75.055	81	618	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	74.9894	57	618	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	74.963	51	618	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.9213	55	618	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	74.8256	66	618	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	74.8213	67	618	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 13:04:06,084] [INFO] DFAST Taxonomy check result was written to GCA_013697265.1_ASM1369726v1_genomic.fna/tc_result.tsv
[2023-06-18 13:04:06,084] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:04:06,084] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:04:06,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference/checkm_data
[2023-06-18 13:04:06,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:04:06,117] [INFO] Task started: CheckM
[2023-06-18 13:04:06,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013697265.1_ASM1369726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013697265.1_ASM1369726v1_genomic.fna/checkm_input GCA_013697265.1_ASM1369726v1_genomic.fna/checkm_result
[2023-06-18 13:04:30,258] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:30,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:30,283] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:30,283] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:30,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013697265.1_ASM1369726v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:30,284] [INFO] Task started: Blastn
[2023-06-18 13:04:30,284] [INFO] Running command: blastn -query GCA_013697265.1_ASM1369726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf20387be-2841-4ebd-98f1-2f02f487a64c/dqc_reference/reference_markers_gtdb.fasta -out GCA_013697265.1_ASM1369726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:31,262] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:31,266] [INFO] Selected 19 target genomes.
[2023-06-18 13:04:31,266] [INFO] Target genome list was writen to GCA_013697265.1_ASM1369726v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:31,273] [INFO] Task started: fastANI
[2023-06-18 13:04:31,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cf4569-83b4-4116-b696-7272dda58ee4/GCA_013697265.1_ASM1369726v1_genomic.fna.gz --refList GCA_013697265.1_ASM1369726v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013697265.1_ASM1369726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:40,895] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:40,909] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:40,909] [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_013697265.1	s__JACCXE01 sp013697265	100.0	610	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDEA01;g__JACCXE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013816725.1	s__JACDEA01 sp013816725	77.9433	103	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDEA01;g__JACDEA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243975.1	s__JAFATL01 sp019243975	76.9046	110	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAFATL01;g__JAFATL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002861595.1	s__GCA-2861595 sp002861595	76.8874	55	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__GCA-2861595;g__GCA-2861595	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.4741	70	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870245.1	s__CAIUKV01 sp016870245	76.1935	78	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.0958	108	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888325.1	s__AC-14 sp005888325	76.0629	109	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__AC-14	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	76.045	115	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870395.1	s__SHUZ01 sp016870395	75.9553	76	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__IMCC26256;g__SHUZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.928	112	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213625.1	s__UBA668 sp016213625	75.9061	84	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	75.8814	53	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_003138855.1	s__Bog-756 sp003138855	75.857	50	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.82	99.61	0.95	0.93	14	-
GCA_006515795.1	s__VFMC01 sp006515795	75.556	54	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.5543	76	618	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:40,912] [INFO] GTDB search result was written to GCA_013697265.1_ASM1369726v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:40,912] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:40,916] [INFO] DFAST_QC result json was written to GCA_013697265.1_ASM1369726v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:40,917] [INFO] DFAST_QC completed!
[2023-06-18 13:04:40,917] [INFO] Total running time: 0h1m1s