[2023-03-17 06:30:49,804] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,804] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference
[2023-03-17 06:30:51,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,357] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,357] [INFO] Running command: cat /var/lib/cwl/stge823b41d-a679-430d-8abb-256951b89542/OceanDNA-b35802.fa | prodigal -d OceanDNA-b35802/cds.fna -a OceanDNA-b35802/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:19,877] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:19,877] [INFO] Task started: HMMsearch
[2023-03-17 06:31:19,877] [INFO] Running command: hmmsearch --tblout OceanDNA-b35802/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference/reference_markers.hmm OceanDNA-b35802/protein.faa > /dev/null
[2023-03-17 06:31:20,095] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:20,096] [INFO] Found 6/6 markers.
[2023-03-17 06:31:20,125] [INFO] Query marker FASTA was written to OceanDNA-b35802/markers.fasta
[2023-03-17 06:31:20,125] [INFO] Task started: Blastn
[2023-03-17 06:31:20,125] [INFO] Running command: blastn -query OceanDNA-b35802/markers.fasta -db /var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference/reference_markers.fasta -out OceanDNA-b35802/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:21,023] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:21,024] [INFO] Selected 29 target genomes.
[2023-03-17 06:31:21,024] [INFO] Target genome list was writen to OceanDNA-b35802/target_genomes.txt
[2023-03-17 06:31:21,037] [INFO] Task started: fastANI
[2023-03-17 06:31:21,037] [INFO] Running command: fastANI --query /var/lib/cwl/stge823b41d-a679-430d-8abb-256951b89542/OceanDNA-b35802.fa --refList OceanDNA-b35802/target_genomes.txt --output OceanDNA-b35802/fastani_result.tsv --threads 1
[2023-03-17 06:31:39,858] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:39,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:39,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:39,874] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:39,874] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:39,874] [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
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.0635	290	1523	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.0594	89	1523	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.0365	160	1523	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	75.9724	151	1523	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.9547	118	1523	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.9435	187	1523	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.9273	171	1523	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.9036	195	1523	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.901	114	1523	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.8718	158	1523	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	75.7987	130	1523	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	75.706	176	1523	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.6799	140	1523	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.6782	135	1523	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.6341	237	1523	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.6322	179	1523	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	75.6199	136	1523	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	75.5891	245	1523	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.5863	210	1523	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.5855	202	1523	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	75.5633	105	1523	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	75.5603	105	1523	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	75.545	164	1523	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	75.5375	85	1523	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	75.492	96	1523	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	75.4598	99	1523	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	75.4527	85	1523	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.367	240	1523	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	75.3338	148	1523	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:39,874] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35802/tc_result.tsv
[2023-03-17 06:31:39,874] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:39,875] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:39,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference/checkm_data
[2023-03-17 06:31:39,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:39,881] [INFO] Task started: CheckM
[2023-03-17 06:31:39,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35802/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35802/checkm_input OceanDNA-b35802/checkm_result
[2023-03-17 06:32:49,920] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:49,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:49,924] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:49,924] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:49,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35802/markers.fasta)
[2023-03-17 06:32:49,924] [INFO] Task started: Blastn
[2023-03-17 06:32:49,924] [INFO] Running command: blastn -query OceanDNA-b35802/markers.fasta -db /var/lib/cwl/stg69fa58f2-dd8d-4efc-8fbf-d99224fc30a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35802/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:51,708] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:51,709] [INFO] Selected 27 target genomes.
[2023-03-17 06:32:51,709] [INFO] Target genome list was writen to OceanDNA-b35802/target_genomes_gtdb.txt
[2023-03-17 06:32:52,348] [INFO] Task started: fastANI
[2023-03-17 06:32:52,348] [INFO] Running command: fastANI --query /var/lib/cwl/stge823b41d-a679-430d-8abb-256951b89542/OceanDNA-b35802.fa --refList OceanDNA-b35802/target_genomes_gtdb.txt --output OceanDNA-b35802/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:33:09,040] [INFO] Task succeeded: fastANI
[2023-03-17 06:33:09,055] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:33:09,055] [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_016719885.1	s__JADJYF01 sp016719885	78.1893	558	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
GCA_001464935.1	s__Ga0077536 sp001464935	76.9904	359	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209015.1	s__JACQWY01 sp016209015	76.8258	378	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JACQWY01	95.0	99.49	99.49	0.94	0.94	2	-
GCA_016874535.1	s__CAIKBL01 sp016874535	76.4661	156	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__CAIKBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694425.1	s__J113 sp003694425	76.2926	85	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J113;f__J113;g__J113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.2442	87	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279065.1	s__Dyella_A sp002279065	76.0919	140	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015494295.1	s__Thiogranum sp015494295	76.0902	130	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	76.0424	180	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.0055	68	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_000327045.1	s__Thioflavicoccus mobilis	75.9546	118	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	75.9003	171	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	75.8697	223	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	75.854	160	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248565.1	s__Stenotrophomonas sp003248565	75.8073	59	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	75.7471	260	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187485.1	s__JADKFD01 sp019187485	75.7066	162	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641285.1	s__Dyella_A thiooxydans	75.5875	170	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342425.1	s__Dokdonella_A fugitiva	75.5678	245	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
GCA_016702655.1	s__CAIKUF01 sp016702655	75.5299	224	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	75.5226	263	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725155.1	s__Tahibacter sp001725155	75.5174	230	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCF_001887595.1	s__Luteibacter rhizovicinus	75.492	96	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012026925.1	s__RPQJ01 sp012026925	75.4763	103	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241895.1	s__Rubrivivax sp018241895	75.4406	218	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187185.1	s__CADEFQ01 sp019187185	75.4109	165	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	98.79	98.79	0.92	0.92	2	-
GCA_019232985.1	s__JAFAMW01 sp019232985	75.2193	213	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:33:09,056] [INFO] GTDB search result was written to OceanDNA-b35802/result_gtdb.tsv
[2023-03-17 06:33:09,056] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:33:09,058] [INFO] DFAST_QC result json was written to OceanDNA-b35802/dqc_result.json
[2023-03-17 06:33:09,059] [INFO] DFAST_QC completed!
[2023-03-17 06:33:09,059] [INFO] Total running time: 0h2m19s