[2023-03-16 04:24:46,334] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference
[2023-03-16 04:24:48,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stgce96d89f-d60f-4245-a3c4-a02f60da4841/OceanDNA-b32602.fa | prodigal -d OceanDNA-b32602/cds.fna -a OceanDNA-b32602/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:14,071] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:14,071] [INFO] Task started: HMMsearch
[2023-03-16 04:25:14,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b32602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference/reference_markers.hmm OceanDNA-b32602/protein.faa > /dev/null
[2023-03-16 04:25:14,399] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:14,400] [INFO] Found 6/6 markers.
[2023-03-16 04:25:14,433] [INFO] Query marker FASTA was written to OceanDNA-b32602/markers.fasta
[2023-03-16 04:25:14,434] [INFO] Task started: Blastn
[2023-03-16 04:25:14,434] [INFO] Running command: blastn -query OceanDNA-b32602/markers.fasta -db /var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference/reference_markers.fasta -out OceanDNA-b32602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:15,528] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:15,529] [INFO] Selected 20 target genomes.
[2023-03-16 04:25:15,530] [INFO] Target genome list was writen to OceanDNA-b32602/target_genomes.txt
[2023-03-16 04:25:15,541] [INFO] Task started: fastANI
[2023-03-16 04:25:15,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgce96d89f-d60f-4245-a3c4-a02f60da4841/OceanDNA-b32602.fa --refList OceanDNA-b32602/target_genomes.txt --output OceanDNA-b32602/fastani_result.tsv --threads 1
[2023-03-16 04:25:36,901] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:36,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:36,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:36,914] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:36,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:25:36,914] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	87.0891	1219	1417	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.8767	582	1417	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.8576	583	1417	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	77.7739	414	1417	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.6165	324	1417	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.5765	307	1417	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.5641	353	1417	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.4795	404	1417	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	77.1037	257	1417	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.0958	445	1417	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	77.0006	409	1417	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.9467	432	1417	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.9118	435	1417	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.903	359	1417	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.8207	450	1417	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.8045	423	1417	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.7209	457	1417	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	75.9912	309	1417	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	75.6683	92	1417	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	75.5072	98	1417	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:36,914] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32602/tc_result.tsv
[2023-03-16 04:25:36,914] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:36,914] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:36,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference/checkm_data
[2023-03-16 04:25:36,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:36,923] [INFO] Task started: CheckM
[2023-03-16 04:25:36,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32602/checkm_input OceanDNA-b32602/checkm_result
[2023-03-16 04:26:38,182] [INFO] Task succeeded: CheckM
[2023-03-16 04:26:38,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.51%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:26:38,186] [INFO] ===== Completeness check finished =====
[2023-03-16 04:26:38,186] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:26:38,186] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32602/markers.fasta)
[2023-03-16 04:26:38,187] [INFO] Task started: Blastn
[2023-03-16 04:26:38,188] [INFO] Running command: blastn -query OceanDNA-b32602/markers.fasta -db /var/lib/cwl/stg1d30a24d-910d-4990-b174-d83e805cd27a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:26:40,243] [INFO] Task succeeded: Blastn
[2023-03-16 04:26:40,502] [INFO] Selected 14 target genomes.
[2023-03-16 04:26:40,502] [INFO] Target genome list was writen to OceanDNA-b32602/target_genomes_gtdb.txt
[2023-03-16 04:26:40,542] [INFO] Task started: fastANI
[2023-03-16 04:26:40,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgce96d89f-d60f-4245-a3c4-a02f60da4841/OceanDNA-b32602.fa --refList OceanDNA-b32602/target_genomes_gtdb.txt --output OceanDNA-b32602/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:55,883] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:55,892] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:26:55,892] [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_014652915.1	s__Thalassobaculum_A fulvum	87.068	1222	1417	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_018401495.1	s__Thalassobaculum_A sp018401495	84.1617	959	1417	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_000171835.1	s__Thalassobaculum_A sp000171835	82.1467	945	1417	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_900102465.1	s__Thalassobaculum litoreum	80.2448	746	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_013203465.1	s__JABMNR01 sp013203465	79.4218	551	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABMNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	77.9075	401	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.8115	591	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000299935.1	s__Oceanibaculum indicum	77.6419	322	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCF_001618175.1	s__Oceanibaculum pacificum	77.5323	313	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	77.0829	494	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	76.9831	266	1417	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_006738645.1	s__Stella humosa	76.9059	434	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	76.8423	447	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722335.1	s__Caulobacter flavus	75.847	277	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:55,893] [INFO] GTDB search result was written to OceanDNA-b32602/result_gtdb.tsv
[2023-03-16 04:26:55,893] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:55,894] [INFO] DFAST_QC result json was written to OceanDNA-b32602/dqc_result.json
[2023-03-16 04:26:55,895] [INFO] DFAST_QC completed!
[2023-03-16 04:26:55,895] [INFO] Total running time: 0h2m10s