[2023-03-15 12:33:51,661] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,661] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference
[2023-03-15 12:33:52,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,844] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,844] [INFO] Running command: cat /var/lib/cwl/stg323c6cda-5da8-45a3-9692-92645ad7ed4f/OceanDNA-b24778.fa | prodigal -d OceanDNA-b24778/cds.fna -a OceanDNA-b24778/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:16,099] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:16,099] [INFO] Task started: HMMsearch
[2023-03-15 12:34:16,100] [INFO] Running command: hmmsearch --tblout OceanDNA-b24778/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference/reference_markers.hmm OceanDNA-b24778/protein.faa > /dev/null
[2023-03-15 12:34:16,307] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:16,308] [INFO] Found 6/6 markers.
[2023-03-15 12:34:16,340] [INFO] Query marker FASTA was written to OceanDNA-b24778/markers.fasta
[2023-03-15 12:34:16,340] [INFO] Task started: Blastn
[2023-03-15 12:34:16,340] [INFO] Running command: blastn -query OceanDNA-b24778/markers.fasta -db /var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference/reference_markers.fasta -out OceanDNA-b24778/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:17,013] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:17,018] [INFO] Selected 25 target genomes.
[2023-03-15 12:34:17,018] [INFO] Target genome list was writen to OceanDNA-b24778/target_genomes.txt
[2023-03-15 12:34:17,035] [INFO] Task started: fastANI
[2023-03-15 12:34:17,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg323c6cda-5da8-45a3-9692-92645ad7ed4f/OceanDNA-b24778.fa --refList OceanDNA-b24778/target_genomes.txt --output OceanDNA-b24778/fastani_result.tsv --threads 1
[2023-03-15 12:34:37,349] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:37,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:37,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:37,362] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:37,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:37,362] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.2894	138	1252	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.1379	135	1252	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.0745	104	1252	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.9771	93	1252	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.97	90	1252	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.9197	167	1252	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.6168	90	1252	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	75.592	53	1252	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.5747	90	1252	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.5118	58	1252	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.4745	102	1252	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.3478	82	1252	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.3462	62	1252	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.3299	72	1252	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.2916	82	1252	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.2788	72	1252	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.2618	69	1252	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.2534	84	1252	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.2505	112	1252	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.122	62	1252	95	below_threshold
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	75.0293	54	1252	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:37,364] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24778/tc_result.tsv
[2023-03-15 12:34:37,366] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:37,366] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:37,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference/checkm_data
[2023-03-15 12:34:37,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:37,375] [INFO] Task started: CheckM
[2023-03-15 12:34:37,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24778/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24778/checkm_input OceanDNA-b24778/checkm_result
[2023-03-15 12:35:34,924] [INFO] Task succeeded: CheckM
[2023-03-15 12:35:34,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:35:34,929] [INFO] ===== Completeness check finished =====
[2023-03-15 12:35:34,929] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:35:34,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24778/markers.fasta)
[2023-03-15 12:35:34,930] [INFO] Task started: Blastn
[2023-03-15 12:35:34,930] [INFO] Running command: blastn -query OceanDNA-b24778/markers.fasta -db /var/lib/cwl/stg5c914b49-2b1f-4621-9613-23d20f289d08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24778/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:36,119] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:36,122] [INFO] Selected 29 target genomes.
[2023-03-15 12:35:36,122] [INFO] Target genome list was writen to OceanDNA-b24778/target_genomes_gtdb.txt
[2023-03-15 12:35:36,649] [INFO] Task started: fastANI
[2023-03-15 12:35:36,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg323c6cda-5da8-45a3-9692-92645ad7ed4f/OceanDNA-b24778.fa --refList OceanDNA-b24778/target_genomes_gtdb.txt --output OceanDNA-b24778/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:56,575] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:56,587] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:56,587] [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_016780745.1	s__JADHLJ01 sp016780745	78.3137	406	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.2894	138	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699735.1	s__JABIRP01 sp018699735	76.1831	82	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABIRP01	95.0	99.37	99.37	0.86	0.86	2	-
GCA_017640745.1	s__Nisaea sp017640745	76.1621	134	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.1347	138	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_014904795.1	s__Nisaea nitritireducens	76.0745	104	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	75.97	90	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	75.9652	145	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426505.1	s__Nisaea denitrificans	75.9612	94	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	75.937	165	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238645.1	s__Bin52 sp002238645	75.8346	128	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Bin52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.6502	61	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.6378	102	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_009694185.1	s__SHVR01 sp009694185	75.582	60	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVR01;f__SHVR01;g__SHVR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	75.5385	103	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941945.1	s__Roseomonas gilardii	75.4809	52	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCA_016869645.1	s__SHVW01 sp016869645	75.4189	70	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990895.1	s__Reyranella sp017990895	75.3764	57	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355985.1	s__Desertibacter sp017355985	75.3466	62	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937115.1	s__Rhodopila globiformis	75.255	68	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:56,589] [INFO] GTDB search result was written to OceanDNA-b24778/result_gtdb.tsv
[2023-03-15 12:35:56,594] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:56,599] [INFO] DFAST_QC result json was written to OceanDNA-b24778/dqc_result.json
[2023-03-15 12:35:56,599] [INFO] DFAST_QC completed!
[2023-03-15 12:35:56,599] [INFO] Total running time: 0h2m5s