[2023-06-08 07:02:45,530] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:02:45,532] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:02:45,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference
[2023-06-08 07:02:47,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:02:47,757] [INFO] Task started: Prodigal
[2023-06-08 07:02:47,758] [INFO] Running command: gunzip -c /var/lib/cwl/stge8a48997-adde-44ba-a748-0f6ef35e68dc/GCA_945891635.1_MiE-16apr19-183_genomic.fna.gz | prodigal -d GCA_945891635.1_MiE-16apr19-183_genomic.fna/cds.fna -a GCA_945891635.1_MiE-16apr19-183_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:02:54,391] [INFO] Task succeeded: Prodigal
[2023-06-08 07:02:54,392] [INFO] Task started: HMMsearch
[2023-06-08 07:02:54,392] [INFO] Running command: hmmsearch --tblout GCA_945891635.1_MiE-16apr19-183_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference/reference_markers.hmm GCA_945891635.1_MiE-16apr19-183_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:02:54,662] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:02:54,664] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge8a48997-adde-44ba-a748-0f6ef35e68dc/GCA_945891635.1_MiE-16apr19-183_genomic.fna.gz]
[2023-06-08 07:02:54,698] [INFO] Query marker FASTA was written to GCA_945891635.1_MiE-16apr19-183_genomic.fna/markers.fasta
[2023-06-08 07:02:54,699] [INFO] Task started: Blastn
[2023-06-08 07:02:54,699] [INFO] Running command: blastn -query GCA_945891635.1_MiE-16apr19-183_genomic.fna/markers.fasta -db /var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference/reference_markers.fasta -out GCA_945891635.1_MiE-16apr19-183_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:55,602] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:55,606] [INFO] Selected 14 target genomes.
[2023-06-08 07:02:55,607] [INFO] Target genome list was writen to GCA_945891635.1_MiE-16apr19-183_genomic.fna/target_genomes.txt
[2023-06-08 07:02:55,610] [INFO] Task started: fastANI
[2023-06-08 07:02:55,610] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a48997-adde-44ba-a748-0f6ef35e68dc/GCA_945891635.1_MiE-16apr19-183_genomic.fna.gz --refList GCA_945891635.1_MiE-16apr19-183_genomic.fna/target_genomes.txt --output GCA_945891635.1_MiE-16apr19-183_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:03:04,852] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:04,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:03:04,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:03:04,865] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 07:03:04,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 07:03:04,865] [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
Sandarakinorhabdus limnophila	strain=DSM 17366	GCA_000420765.1	210512	210512	type	True	95.5464	578	613	95	conclusive
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	85.4825	487	613	95	below_threshold
Sandarakinorhabdus cyanobacteriorum	strain=TH057	GCA_002251755.1	1981098	1981098	type	True	83.4745	520	613	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	82.7553	406	613	95	below_threshold
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	78.4324	296	613	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.8915	273	613	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.1409	179	613	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.112	163	613	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	76.8374	142	613	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.7973	146	613	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.7405	130	613	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.7062	104	613	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	76.6171	128	613	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	75.9504	89	613	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:03:04,867] [INFO] DFAST Taxonomy check result was written to GCA_945891635.1_MiE-16apr19-183_genomic.fna/tc_result.tsv
[2023-06-08 07:03:04,868] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:03:04,868] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:03:04,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference/checkm_data
[2023-06-08 07:03:04,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:03:04,898] [INFO] Task started: CheckM
[2023-06-08 07:03:04,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945891635.1_MiE-16apr19-183_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945891635.1_MiE-16apr19-183_genomic.fna/checkm_input GCA_945891635.1_MiE-16apr19-183_genomic.fna/checkm_result
[2023-06-08 07:03:31,713] [INFO] Task succeeded: CheckM
[2023-06-08 07:03:31,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:03:31,739] [INFO] ===== Completeness check finished =====
[2023-06-08 07:03:31,739] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:03:31,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945891635.1_MiE-16apr19-183_genomic.fna/markers.fasta)
[2023-06-08 07:03:31,740] [INFO] Task started: Blastn
[2023-06-08 07:03:31,740] [INFO] Running command: blastn -query GCA_945891635.1_MiE-16apr19-183_genomic.fna/markers.fasta -db /var/lib/cwl/stg42cf92e6-cac2-4a3b-8a64-54fe81d6e954/dqc_reference/reference_markers_gtdb.fasta -out GCA_945891635.1_MiE-16apr19-183_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:03:33,021] [INFO] Task succeeded: Blastn
[2023-06-08 07:03:33,028] [INFO] Selected 7 target genomes.
[2023-06-08 07:03:33,028] [INFO] Target genome list was writen to GCA_945891635.1_MiE-16apr19-183_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:03:33,036] [INFO] Task started: fastANI
[2023-06-08 07:03:33,036] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a48997-adde-44ba-a748-0f6ef35e68dc/GCA_945891635.1_MiE-16apr19-183_genomic.fna.gz --refList GCA_945891635.1_MiE-16apr19-183_genomic.fna/target_genomes_gtdb.txt --output GCA_945891635.1_MiE-16apr19-183_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:03:37,649] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:37,660] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:03:37,660] [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_000420765.1	s__Sandarakinorhabdus limnophila	95.5464	578	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.49	96.49	0.92	0.92	2	conclusive
GCA_002280855.1	s__Sandarakinorhabdus sp002280855	94.2365	579	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.11	96.11	0.96	0.96	2	-
GCF_000331225.1	s__Sandarakinorhabdus sp000331225	87.9882	563	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733735.1	s__Sandarakinorhabdus oryzae	85.498	485	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251755.1	s__Sandarakinorhabdus cyanobacteriorum	83.5437	516	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.87	96.87	0.91	0.91	2	-
GCA_018970445.1	s__Sandarakinorhabdus sp018970445	83.4512	513	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994245.1	s__Sandarakinorhabdus rubra	82.7678	405	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:03:37,662] [INFO] GTDB search result was written to GCA_945891635.1_MiE-16apr19-183_genomic.fna/result_gtdb.tsv
[2023-06-08 07:03:37,662] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:03:37,666] [INFO] DFAST_QC result json was written to GCA_945891635.1_MiE-16apr19-183_genomic.fna/dqc_result.json
[2023-06-08 07:03:37,666] [INFO] DFAST_QC completed!
[2023-06-08 07:03:37,666] [INFO] Total running time: 0h0m52s