[2023-03-18 01:35:16,898] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:35:16,898] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:35:16,898] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference
[2023-03-18 01:35:18,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:35:18,369] [INFO] Task started: Prodigal
[2023-03-18 01:35:18,369] [INFO] Running command: cat /var/lib/cwl/stg5b36ad59-6098-43c7-a5d1-5b0aae576af8/OceanDNA-b32265.fa | prodigal -d OceanDNA-b32265/cds.fna -a OceanDNA-b32265/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:35:32,447] [INFO] Task succeeded: Prodigal
[2023-03-18 01:35:32,448] [INFO] Task started: HMMsearch
[2023-03-18 01:35:32,448] [INFO] Running command: hmmsearch --tblout OceanDNA-b32265/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference/reference_markers.hmm OceanDNA-b32265/protein.faa > /dev/null
[2023-03-18 01:35:32,629] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:35:32,629] [INFO] Found 6/6 markers.
[2023-03-18 01:35:32,648] [INFO] Query marker FASTA was written to OceanDNA-b32265/markers.fasta
[2023-03-18 01:35:32,649] [INFO] Task started: Blastn
[2023-03-18 01:35:32,649] [INFO] Running command: blastn -query OceanDNA-b32265/markers.fasta -db /var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference/reference_markers.fasta -out OceanDNA-b32265/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:35:33,322] [INFO] Task succeeded: Blastn
[2023-03-18 01:35:33,323] [INFO] Selected 23 target genomes.
[2023-03-18 01:35:33,323] [INFO] Target genome list was writen to OceanDNA-b32265/target_genomes.txt
[2023-03-18 01:35:33,337] [INFO] Task started: fastANI
[2023-03-18 01:35:33,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b36ad59-6098-43c7-a5d1-5b0aae576af8/OceanDNA-b32265.fa --refList OceanDNA-b32265/target_genomes.txt --output OceanDNA-b32265/fastani_result.tsv --threads 1
[2023-03-18 01:35:47,040] [INFO] Task succeeded: fastANI
[2023-03-18 01:35:47,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:35:47,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:35:47,053] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:35:47,053] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:35:47,053] [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 flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	82.5755	511	744	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	77.8824	268	744	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.726	216	744	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.7143	247	744	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.6273	208	744	95	below_threshold
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	76.8252	104	744	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	76.7053	75	744	95	below_threshold
Novosphingopyxis iocasae	strain=PB63	GCA_014334095.1	2762729	2762729	type	True	76.6339	99	744	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	76.5656	133	744	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	76.563	112	744	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	76.5319	104	744	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	76.4884	79	744	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	76.4632	89	744	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.3512	92	744	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	76.3339	117	744	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	76.3087	74	744	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	76.3001	108	744	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.2555	99	744	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	76.2491	67	744	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.2234	96	744	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	76.0786	63	744	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	75.9665	77	744	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	75.9595	79	744	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:35:47,054] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32265/tc_result.tsv
[2023-03-18 01:35:47,056] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:35:47,056] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:35:47,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference/checkm_data
[2023-03-18 01:35:47,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:35:47,061] [INFO] Task started: CheckM
[2023-03-18 01:35:47,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32265/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32265/checkm_input OceanDNA-b32265/checkm_result
[2023-03-18 01:36:25,835] [INFO] Task succeeded: CheckM
[2023-03-18 01:36:25,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.98%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:36:25,859] [INFO] ===== Completeness check finished =====
[2023-03-18 01:36:25,859] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:36:25,859] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32265/markers.fasta)
[2023-03-18 01:36:25,860] [INFO] Task started: Blastn
[2023-03-18 01:36:25,860] [INFO] Running command: blastn -query OceanDNA-b32265/markers.fasta -db /var/lib/cwl/stgd5c573b4-0bed-4c24-96bc-cd8b33a90733/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32265/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:36:27,022] [INFO] Task succeeded: Blastn
[2023-03-18 01:36:27,026] [INFO] Selected 11 target genomes.
[2023-03-18 01:36:27,026] [INFO] Target genome list was writen to OceanDNA-b32265/target_genomes_gtdb.txt
[2023-03-18 01:36:27,035] [INFO] Task started: fastANI
[2023-03-18 01:36:27,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b36ad59-6098-43c7-a5d1-5b0aae576af8/OceanDNA-b32265.fa --refList OceanDNA-b32265/target_genomes_gtdb.txt --output OceanDNA-b32265/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:36:34,585] [INFO] Task succeeded: fastANI
[2023-03-18 01:36:34,592] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:36:34,592] [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_018067055.1	s__Parasphingorhabdus sp018067055	97.7951	477	744	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_002783865.1	s__Parasphingorhabdus sp002783865	85.548	465	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	84.2105	564	744	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	83.9997	548	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204445.1	s__Parasphingorhabdus sp013204445	83.2752	365	744	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	83.238	536	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	82.643	514	744	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	82.5755	511	744	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	82.5634	434	744	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	82.3915	532	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	82.1572	533	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:36:34,596] [INFO] GTDB search result was written to OceanDNA-b32265/result_gtdb.tsv
[2023-03-18 01:36:34,597] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:36:34,600] [INFO] DFAST_QC result json was written to OceanDNA-b32265/dqc_result.json
[2023-03-18 01:36:34,600] [INFO] DFAST_QC completed!
[2023-03-18 01:36:34,600] [INFO] Total running time: 0h1m18s