[2023-03-17 01:44:57,158] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,158] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference
[2023-03-17 01:44:59,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:44:59,094] [INFO] Task started: Prodigal
[2023-03-17 01:44:59,094] [INFO] Running command: cat /var/lib/cwl/stg3e680bff-0e42-4a67-8e1d-706b8eb4871d/OceanDNA-b33061.fa | prodigal -d OceanDNA-b33061/cds.fna -a OceanDNA-b33061/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:19,883] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:19,884] [INFO] Task started: HMMsearch
[2023-03-17 01:45:19,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b33061/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference/reference_markers.hmm OceanDNA-b33061/protein.faa > /dev/null
[2023-03-17 01:45:20,078] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:20,078] [INFO] Found 6/6 markers.
[2023-03-17 01:45:20,105] [INFO] Query marker FASTA was written to OceanDNA-b33061/markers.fasta
[2023-03-17 01:45:20,106] [INFO] Task started: Blastn
[2023-03-17 01:45:20,106] [INFO] Running command: blastn -query OceanDNA-b33061/markers.fasta -db /var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference/reference_markers.fasta -out OceanDNA-b33061/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:20,779] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:20,780] [INFO] Selected 31 target genomes.
[2023-03-17 01:45:20,780] [INFO] Target genome list was writen to OceanDNA-b33061/target_genomes.txt
[2023-03-17 01:45:20,800] [INFO] Task started: fastANI
[2023-03-17 01:45:20,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e680bff-0e42-4a67-8e1d-706b8eb4871d/OceanDNA-b33061.fa --refList OceanDNA-b33061/target_genomes.txt --output OceanDNA-b33061/fastani_result.tsv --threads 1
[2023-03-17 01:45:42,356] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:42,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:42,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:42,366] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:42,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:45:42,367] [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 pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.9461	115	1104	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.7642	74	1104	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.5435	52	1104	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.5238	107	1104	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	75.4125	56	1104	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.3838	102	1104	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.3429	96	1104	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.2506	57	1104	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.2254	88	1104	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.218	98	1104	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.088	93	1104	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.0878	93	1104	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	75.0412	53	1104	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	75.0287	58	1104	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	74.9865	59	1104	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:45:42,367] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33061/tc_result.tsv
[2023-03-17 01:45:42,367] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:42,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:42,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference/checkm_data
[2023-03-17 01:45:42,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:42,374] [INFO] Task started: CheckM
[2023-03-17 01:45:42,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33061/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33061/checkm_input OceanDNA-b33061/checkm_result
[2023-03-17 01:46:34,508] [INFO] Task succeeded: CheckM
[2023-03-17 01:46:34,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:46:34,511] [INFO] ===== Completeness check finished =====
[2023-03-17 01:46:34,511] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:46:34,512] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33061/markers.fasta)
[2023-03-17 01:46:34,513] [INFO] Task started: Blastn
[2023-03-17 01:46:34,513] [INFO] Running command: blastn -query OceanDNA-b33061/markers.fasta -db /var/lib/cwl/stg39974eb7-4140-429c-b4c9-d8c939ed8223/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33061/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:46:35,651] [INFO] Task succeeded: Blastn
[2023-03-17 01:46:35,652] [INFO] Selected 30 target genomes.
[2023-03-17 01:46:35,652] [INFO] Target genome list was writen to OceanDNA-b33061/target_genomes_gtdb.txt
[2023-03-17 01:46:36,441] [INFO] Task started: fastANI
[2023-03-17 01:46:36,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e680bff-0e42-4a67-8e1d-706b8eb4871d/OceanDNA-b33061.fa --refList OceanDNA-b33061/target_genomes_gtdb.txt --output OceanDNA-b33061/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:46:55,995] [INFO] Task succeeded: fastANI
[2023-03-17 01:46:56,005] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:46:56,005] [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_012103325.1	s__GCA-2717185 sp012103325	76.7777	187	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937525.1	s__MarineAlpha4-Bin1 sp002937525	76.7742	149	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__MarineAlpha4-Bin1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_015222795.1	s__JADFVY01 sp015222795	76.1257	57	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__JADFVY01;g__JADFVY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	75.8726	100	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.629	68	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792605.1	s__JAEULC01 sp016792605	75.6119	85	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853455.1	s__Phaeospirillum sp903853455	75.4944	55	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.4396	89	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	75.3838	102	1104	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_017876115.1	s__Azospirillum picis	75.3532	95	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794165.1	s__Dongia sp016794165	75.3397	53	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	75.3342	76	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.3206	116	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	75.218	98	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_007827795.1	s__Azospirillum brasilense_E	75.1806	79	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_003119195.2	s__Azospirillum baldaniorum	75.0878	93	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_003122215.1	s__Pararhodobacter marinus	75.0412	53	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:46:56,005] [INFO] GTDB search result was written to OceanDNA-b33061/result_gtdb.tsv
[2023-03-17 01:46:56,006] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:46:56,007] [INFO] DFAST_QC result json was written to OceanDNA-b33061/dqc_result.json
[2023-03-17 01:46:56,008] [INFO] DFAST_QC completed!
[2023-03-17 01:46:56,008] [INFO] Total running time: 0h1m59s