[2023-03-16 07:34:40,383] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,384] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference
[2023-03-16 07:34:41,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:41,796] [INFO] Task started: Prodigal
[2023-03-16 07:34:41,796] [INFO] Running command: cat /var/lib/cwl/stgf34bf82f-d411-4cb1-afcf-4ef9f6965ec8/OceanDNA-b24067.fa | prodigal -d OceanDNA-b24067/cds.fna -a OceanDNA-b24067/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:34:54,768] [INFO] Task succeeded: Prodigal
[2023-03-16 07:34:54,768] [INFO] Task started: HMMsearch
[2023-03-16 07:34:54,769] [INFO] Running command: hmmsearch --tblout OceanDNA-b24067/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference/reference_markers.hmm OceanDNA-b24067/protein.faa > /dev/null
[2023-03-16 07:34:54,963] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:34:54,964] [INFO] Found 6/6 markers.
[2023-03-16 07:34:54,985] [INFO] Query marker FASTA was written to OceanDNA-b24067/markers.fasta
[2023-03-16 07:34:54,986] [INFO] Task started: Blastn
[2023-03-16 07:34:54,986] [INFO] Running command: blastn -query OceanDNA-b24067/markers.fasta -db /var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference/reference_markers.fasta -out OceanDNA-b24067/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:34:55,684] [INFO] Task succeeded: Blastn
[2023-03-16 07:34:55,684] [INFO] Selected 33 target genomes.
[2023-03-16 07:34:55,685] [INFO] Target genome list was writen to OceanDNA-b24067/target_genomes.txt
[2023-03-16 07:34:55,834] [INFO] Task started: fastANI
[2023-03-16 07:34:55,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgf34bf82f-d411-4cb1-afcf-4ef9f6965ec8/OceanDNA-b24067.fa --refList OceanDNA-b24067/target_genomes.txt --output OceanDNA-b24067/fastani_result.tsv --threads 1
[2023-03-16 07:35:20,934] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:20,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:20,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:20,944] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:20,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:35:20,944] [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
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.8643	52	674	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.7975	55	674	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.6307	74	674	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.6306	74	674	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.5367	65	674	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4929	64	674	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.4929	64	674	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.4254	59	674	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.3814	63	674	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.3601	65	674	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.3116	72	674	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.2982	67	674	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.2772	62	674	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.2029	74	674	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:35:20,944] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24067/tc_result.tsv
[2023-03-16 07:35:20,944] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:20,944] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:20,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference/checkm_data
[2023-03-16 07:35:20,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:20,950] [INFO] Task started: CheckM
[2023-03-16 07:35:20,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24067/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24067/checkm_input OceanDNA-b24067/checkm_result
[2023-03-16 07:35:56,514] [INFO] Task succeeded: CheckM
[2023-03-16 07:35:56,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:35:56,518] [INFO] ===== Completeness check finished =====
[2023-03-16 07:35:56,518] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:35:56,518] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24067/markers.fasta)
[2023-03-16 07:35:56,520] [INFO] Task started: Blastn
[2023-03-16 07:35:56,520] [INFO] Running command: blastn -query OceanDNA-b24067/markers.fasta -db /var/lib/cwl/stg86f91563-bc28-48b3-9c40-6aaa2a40826b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24067/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:57,922] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:57,924] [INFO] Selected 29 target genomes.
[2023-03-16 07:35:57,924] [INFO] Target genome list was writen to OceanDNA-b24067/target_genomes_gtdb.txt
[2023-03-16 07:35:59,170] [INFO] Task started: fastANI
[2023-03-16 07:35:59,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgf34bf82f-d411-4cb1-afcf-4ef9f6965ec8/OceanDNA-b24067.fa --refList OceanDNA-b24067/target_genomes_gtdb.txt --output OceanDNA-b24067/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:18,150] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:18,156] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:36:18,156] [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_018660305.1	s__JABJKO01 sp018660305	77.0923	182	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCA_009377375.1	s__WHUE01 sp009377375	76.9516	193	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103315.1	s__WLWZ01 sp012103315	76.1771	62	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WLWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.8443	64	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	75.7779	88	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923315.1	s__Azospirillum sp003116065	75.616	57	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_003349955.1	s__Azospirillum brasilense_B	75.5725	53	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_006739055.1	s__Stella vacuolata	75.2497	65	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.2302	55	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:18,156] [INFO] GTDB search result was written to OceanDNA-b24067/result_gtdb.tsv
[2023-03-16 07:36:18,157] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:18,158] [INFO] DFAST_QC result json was written to OceanDNA-b24067/dqc_result.json
[2023-03-16 07:36:18,158] [INFO] DFAST_QC completed!
[2023-03-16 07:36:18,158] [INFO] Total running time: 0h1m38s