[2023-06-29 19:44:54,759] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:44:54,763] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:44:54,763] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference
[2023-06-29 19:44:56,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:44:56,068] [INFO] Task started: Prodigal
[2023-06-29 19:44:56,069] [INFO] Running command: gunzip -c /var/lib/cwl/stgc186d1bc-abac-48ac-be1e-8beae6b50c1a/GCA_011371355.1_ASM1137135v1_genomic.fna.gz | prodigal -d GCA_011371355.1_ASM1137135v1_genomic.fna/cds.fna -a GCA_011371355.1_ASM1137135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:45:01,459] [INFO] Task succeeded: Prodigal
[2023-06-29 19:45:01,460] [INFO] Task started: HMMsearch
[2023-06-29 19:45:01,460] [INFO] Running command: hmmsearch --tblout GCA_011371355.1_ASM1137135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference/reference_markers.hmm GCA_011371355.1_ASM1137135v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:45:01,745] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:45:01,747] [INFO] Found 6/6 markers.
[2023-06-29 19:45:01,772] [INFO] Query marker FASTA was written to GCA_011371355.1_ASM1137135v1_genomic.fna/markers.fasta
[2023-06-29 19:45:01,772] [INFO] Task started: Blastn
[2023-06-29 19:45:01,772] [INFO] Running command: blastn -query GCA_011371355.1_ASM1137135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference/reference_markers.fasta -out GCA_011371355.1_ASM1137135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:02,549] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:02,553] [INFO] Selected 25 target genomes.
[2023-06-29 19:45:02,554] [INFO] Target genome list was writen to GCA_011371355.1_ASM1137135v1_genomic.fna/target_genomes.txt
[2023-06-29 19:45:02,558] [INFO] Task started: fastANI
[2023-06-29 19:45:02,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgc186d1bc-abac-48ac-be1e-8beae6b50c1a/GCA_011371355.1_ASM1137135v1_genomic.fna.gz --refList GCA_011371355.1_ASM1137135v1_genomic.fna/target_genomes.txt --output GCA_011371355.1_ASM1137135v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:45:26,415] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:26,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:45:26,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:45:26,434] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:45:26,435] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:45:26,435] [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
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	75.3218	104	692	95	below_threshold
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	75.3165	98	692	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.2595	138	692	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	75.2585	153	692	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	75.243	141	692	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	75.2378	123	692	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	75.1625	58	692	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	75.1507	179	692	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	75.1451	202	692	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	75.1368	64	692	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	75.1137	143	692	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	75.0483	109	692	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	75.0152	65	692	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	75.0115	191	692	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	75.0078	125	692	95	below_threshold
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	74.9695	87	692	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	74.9507	50	692	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	74.9485	119	692	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	74.9189	148	692	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	74.8483	197	692	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	74.8237	225	692	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.7747	59	692	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	74.7483	87	692	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.622	142	692	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:45:26,439] [INFO] DFAST Taxonomy check result was written to GCA_011371355.1_ASM1137135v1_genomic.fna/tc_result.tsv
[2023-06-29 19:45:26,440] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:45:26,440] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:45:26,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference/checkm_data
[2023-06-29 19:45:26,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:45:26,480] [INFO] Task started: CheckM
[2023-06-29 19:45:26,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011371355.1_ASM1137135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011371355.1_ASM1137135v1_genomic.fna/checkm_input GCA_011371355.1_ASM1137135v1_genomic.fna/checkm_result
[2023-06-29 19:45:54,993] [INFO] Task succeeded: CheckM
[2023-06-29 19:45:54,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:45:55,017] [INFO] ===== Completeness check finished =====
[2023-06-29 19:45:55,017] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:45:55,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011371355.1_ASM1137135v1_genomic.fna/markers.fasta)
[2023-06-29 19:45:55,018] [INFO] Task started: Blastn
[2023-06-29 19:45:55,018] [INFO] Running command: blastn -query GCA_011371355.1_ASM1137135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1c2b911-616b-423f-aeb2-8b4f02a16ed3/dqc_reference/reference_markers_gtdb.fasta -out GCA_011371355.1_ASM1137135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:56,082] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:56,088] [INFO] Selected 21 target genomes.
[2023-06-29 19:45:56,088] [INFO] Target genome list was writen to GCA_011371355.1_ASM1137135v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:45:56,102] [INFO] Task started: fastANI
[2023-06-29 19:45:56,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgc186d1bc-abac-48ac-be1e-8beae6b50c1a/GCA_011371355.1_ASM1137135v1_genomic.fna.gz --refList GCA_011371355.1_ASM1137135v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011371355.1_ASM1137135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:46:05,980] [INFO] Task succeeded: fastANI
[2023-06-29 19:46:05,996] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:46:05,996] [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_011371355.1	s__DRQR01 sp011371355	100.0	685	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__DRQR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013695075.1	s__JACDBE01 sp013695075	76.6361	111	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__JACDBE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242515.1	s__ZC4RG35 sp003242515	76.6185	105	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__ZC4RG35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450985.1	s__UBA6912 sp002450985	76.5199	177	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__UBA6912	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018821365.1	s__JAHJML01 sp018821365	76.4943	104	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__JAHJML01	95.0	99.66	99.66	0.91	0.91	2	-
GCA_013001485.1	s__JABDIW01 sp013001485	76.3484	72	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__JABDIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215655.1	s__UBA11373 sp016215655	76.3333	116	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__UBA11373	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577575.1	s__ZC4RG17 sp017577575	76.2504	171	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__ZC4RG17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767695.1	s__RBG-16-68-21 sp001767695	76.1854	107	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__RBG-16-68-21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151445.1	s__BMS3BBIN02 sp013151445	75.9303	51	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__BMS3BBIN02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004283105.1	s__SHLN01 sp004283105	75.612	57	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__SHLN01;g__SHLN01	95.0	99.09	98.81	0.83	0.70	6	-
GCA_003486285.1	s__UBA11373 sp003486285	75.5413	65	692	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__UBA11373	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133465.1	s__SLMP01 sp007133465	75.2777	103	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLMP01	95.0	99.22	99.05	0.81	0.81	3	-
GCF_000559025.1	s__Luteimonas huabeiensis	74.7677	60	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:46:05,998] [INFO] GTDB search result was written to GCA_011371355.1_ASM1137135v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:46:05,999] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:46:06,003] [INFO] DFAST_QC result json was written to GCA_011371355.1_ASM1137135v1_genomic.fna/dqc_result.json
[2023-06-29 19:46:06,004] [INFO] DFAST_QC completed!
[2023-06-29 19:46:06,004] [INFO] Total running time: 0h1m11s