[2024-01-24 13:13:31,035] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:31,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:31,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference
[2024-01-24 13:13:32,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:32,230] [INFO] Task started: Prodigal
[2024-01-24 13:13:32,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg3aad45bf-aba8-4e0c-9f97-8ba048687082/GCF_017498565.1_ASM1749856v1_genomic.fna.gz | prodigal -d GCF_017498565.1_ASM1749856v1_genomic.fna/cds.fna -a GCF_017498565.1_ASM1749856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:44,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:44,304] [INFO] Task started: HMMsearch
[2024-01-24 13:13:44,304] [INFO] Running command: hmmsearch --tblout GCF_017498565.1_ASM1749856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference/reference_markers.hmm GCF_017498565.1_ASM1749856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:44,575] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:44,577] [INFO] Found 6/6 markers.
[2024-01-24 13:13:44,617] [INFO] Query marker FASTA was written to GCF_017498565.1_ASM1749856v1_genomic.fna/markers.fasta
[2024-01-24 13:13:44,618] [INFO] Task started: Blastn
[2024-01-24 13:13:44,618] [INFO] Running command: blastn -query GCF_017498565.1_ASM1749856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference/reference_markers.fasta -out GCF_017498565.1_ASM1749856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:45,218] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:45,222] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:45,222] [INFO] Target genome list was writen to GCF_017498565.1_ASM1749856v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:45,369] [INFO] Task started: fastANI
[2024-01-24 13:13:45,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aad45bf-aba8-4e0c-9f97-8ba048687082/GCF_017498565.1_ASM1749856v1_genomic.fna.gz --refList GCF_017498565.1_ASM1749856v1_genomic.fna/target_genomes.txt --output GCF_017498565.1_ASM1749856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:58,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:58,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:58,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:58,098] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:58,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:58,098] [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 cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	100.0	1259	1259	95	conclusive
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	81.9491	784	1259	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.158	370	1259	95	below_threshold
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	78.1276	354	1259	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.0663	359	1259	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	76.7544	80	1259	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.5209	88	1259	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.4793	70	1259	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	76.3477	104	1259	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.2943	97	1259	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.2726	75	1259	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	76.211	77	1259	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	75.6824	60	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:58,100] [INFO] DFAST Taxonomy check result was written to GCF_017498565.1_ASM1749856v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:58,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:58,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:58,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference/checkm_data
[2024-01-24 13:13:58,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:58,138] [INFO] Task started: CheckM
[2024-01-24 13:13:58,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017498565.1_ASM1749856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017498565.1_ASM1749856v1_genomic.fna/checkm_input GCF_017498565.1_ASM1749856v1_genomic.fna/checkm_result
[2024-01-24 13:14:37,460] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:37,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:37,483] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:37,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:37,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017498565.1_ASM1749856v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:37,485] [INFO] Task started: Blastn
[2024-01-24 13:14:37,485] [INFO] Running command: blastn -query GCF_017498565.1_ASM1749856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfc8393d-d9d1-4563-95d1-b7996998da1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017498565.1_ASM1749856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:38,348] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:38,352] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:38,352] [INFO] Target genome list was writen to GCF_017498565.1_ASM1749856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:38,400] [INFO] Task started: fastANI
[2024-01-24 13:14:38,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aad45bf-aba8-4e0c-9f97-8ba048687082/GCF_017498565.1_ASM1749856v1_genomic.fna.gz --refList GCF_017498565.1_ASM1749856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017498565.1_ASM1749856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:47,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:47,710] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:47,710] [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_017498565.1	s__Parasphingorhabdus sp017498565	100.0	1259	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900258045.1	s__Parasphingorhabdus sp900258045	81.8274	716	1259	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	81.2894	708	1259	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	79.04	378	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128895.1	s__Parasphingorhabdus marina	78.1641	368	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479715.1	s__Parasphingorhabdus sp905479715	78.1468	310	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650955.1	s__Parasphingorhabdus sp001650955	78.1169	363	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	78.1098	351	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516475.1	s__Parasphingorhabdus sp012516475	78.0699	358	1259	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	78.0546	358	1259	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	77.9873	321	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255985.1	s__Sphingorhabdus_B sp002255985	75.785	68	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.49	98.44	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:47,712] [INFO] GTDB search result was written to GCF_017498565.1_ASM1749856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:47,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:47,717] [INFO] DFAST_QC result json was written to GCF_017498565.1_ASM1749856v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:47,717] [INFO] DFAST_QC completed!
[2024-01-24 13:14:47,717] [INFO] Total running time: 0h1m17s