[2024-01-24 13:40:55,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference
[2024-01-24 13:40:56,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,775] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d074aba-ca91-4cd8-af88-cec7f2b21143/GCF_012516475.1_ASM1251647v1_genomic.fna.gz | prodigal -d GCF_012516475.1_ASM1251647v1_genomic.fna/cds.fna -a GCF_012516475.1_ASM1251647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,807] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,807] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,807] [INFO] Running command: hmmsearch --tblout GCF_012516475.1_ASM1251647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference/reference_markers.hmm GCF_012516475.1_ASM1251647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,092] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,093] [INFO] Found 6/6 markers.
[2024-01-24 13:41:06,127] [INFO] Query marker FASTA was written to GCF_012516475.1_ASM1251647v1_genomic.fna/markers.fasta
[2024-01-24 13:41:06,127] [INFO] Task started: Blastn
[2024-01-24 13:41:06,127] [INFO] Running command: blastn -query GCF_012516475.1_ASM1251647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference/reference_markers.fasta -out GCF_012516475.1_ASM1251647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,822] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,827] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:06,827] [INFO] Target genome list was writen to GCF_012516475.1_ASM1251647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:06,837] [INFO] Task started: fastANI
[2024-01-24 13:41:06,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d074aba-ca91-4cd8-af88-cec7f2b21143/GCF_012516475.1_ASM1251647v1_genomic.fna.gz --refList GCF_012516475.1_ASM1251647v1_genomic.fna/target_genomes.txt --output GCF_012516475.1_ASM1251647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:17,936] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:17,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:17,947] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:17,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:17,947] [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
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	100.0	1089	1089	95	conclusive
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	78.5732	391	1089	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.1939	344	1089	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.9538	336	1089	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	77.7753	296	1089	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.6062	56	1089	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	76.6054	73	1089	95	below_threshold
Aquisediminimonas profunda	strain=DS48-3	GCA_019443285.1	1550733	1550733	type	True	76.5906	50	1089	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	76.5389	112	1089	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.517	92	1089	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	76.4987	96	1089	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.2109	96	1089	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.1454	71	1089	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.1197	73	1089	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	76.0632	76	1089	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	75.8654	50	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,948] [INFO] DFAST Taxonomy check result was written to GCF_012516475.1_ASM1251647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:17,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:17,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:17,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference/checkm_data
[2024-01-24 13:41:17,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:17,984] [INFO] Task started: CheckM
[2024-01-24 13:41:17,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012516475.1_ASM1251647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012516475.1_ASM1251647v1_genomic.fna/checkm_input GCF_012516475.1_ASM1251647v1_genomic.fna/checkm_result
[2024-01-24 13:41:47,289] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:47,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,304] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:47,304] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:47,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012516475.1_ASM1251647v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:47,305] [INFO] Task started: Blastn
[2024-01-24 13:41:47,305] [INFO] Running command: blastn -query GCF_012516475.1_ASM1251647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10901eb2-5200-4c8c-983a-ee115901dac3/dqc_reference/reference_markers_gtdb.fasta -out GCF_012516475.1_ASM1251647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:48,541] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:48,544] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:48,544] [INFO] Target genome list was writen to GCF_012516475.1_ASM1251647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:48,554] [INFO] Task started: fastANI
[2024-01-24 13:41:48,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d074aba-ca91-4cd8-af88-cec7f2b21143/GCF_012516475.1_ASM1251647v1_genomic.fna.gz --refList GCF_012516475.1_ASM1251647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012516475.1_ASM1251647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:59,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:59,701] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:59,702] [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_012516475.1	s__Parasphingorhabdus sp012516475	100.0	1089	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001650955.1	s__Parasphingorhabdus sp001650955	78.4823	359	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	78.4123	379	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	78.3558	364	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	78.3441	378	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	78.3231	349	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	78.2354	398	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_017498565.1	s__Parasphingorhabdus sp017498565	78.187	344	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	78.1689	311	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCF_900258045.1	s__Parasphingorhabdus sp900258045	78.0364	331	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900149705.1	s__Parasphingorhabdus sp900149705	77.9296	328	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478735.1	s__Parasphingorhabdus sp015478735	77.7301	248	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005518185.1	s__Chakrabartia godavariana	76.5725	62	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003431825.1	s__Blastomonas fulva	76.5389	112	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	98.01	97.97	0.88	0.85	3	-
GCF_003201955.1	s__Blastomonas natatoria	76.3552	106	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,703] [INFO] GTDB search result was written to GCF_012516475.1_ASM1251647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:59,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:59,706] [INFO] DFAST_QC result json was written to GCF_012516475.1_ASM1251647v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:59,706] [INFO] DFAST_QC completed!
[2024-01-24 13:41:59,707] [INFO] Total running time: 0h1m4s