[2023-06-07 23:37:25,939] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:37:25,942] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:37:25,942] [INFO] DQC Reference Directory: /var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference
[2023-06-07 23:37:27,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:37:27,161] [INFO] Task started: Prodigal
[2023-06-07 23:37:27,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd34a6e6-e82c-421b-b24a-ff3fffc9921c/GCA_945903705.1_TH-11nov19-269_genomic.fna.gz | prodigal -d GCA_945903705.1_TH-11nov19-269_genomic.fna/cds.fna -a GCA_945903705.1_TH-11nov19-269_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:37:36,074] [INFO] Task succeeded: Prodigal
[2023-06-07 23:37:36,074] [INFO] Task started: HMMsearch
[2023-06-07 23:37:36,074] [INFO] Running command: hmmsearch --tblout GCA_945903705.1_TH-11nov19-269_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference/reference_markers.hmm GCA_945903705.1_TH-11nov19-269_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:37:36,337] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:37:36,339] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcd34a6e6-e82c-421b-b24a-ff3fffc9921c/GCA_945903705.1_TH-11nov19-269_genomic.fna.gz]
[2023-06-07 23:37:36,371] [INFO] Query marker FASTA was written to GCA_945903705.1_TH-11nov19-269_genomic.fna/markers.fasta
[2023-06-07 23:37:36,372] [INFO] Task started: Blastn
[2023-06-07 23:37:36,372] [INFO] Running command: blastn -query GCA_945903705.1_TH-11nov19-269_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference/reference_markers.fasta -out GCA_945903705.1_TH-11nov19-269_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:37:37,095] [INFO] Task succeeded: Blastn
[2023-06-07 23:37:37,100] [INFO] Selected 33 target genomes.
[2023-06-07 23:37:37,100] [INFO] Target genome list was writen to GCA_945903705.1_TH-11nov19-269_genomic.fna/target_genomes.txt
[2023-06-07 23:37:37,103] [INFO] Task started: fastANI
[2023-06-07 23:37:37,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd34a6e6-e82c-421b-b24a-ff3fffc9921c/GCA_945903705.1_TH-11nov19-269_genomic.fna.gz --refList GCA_945903705.1_TH-11nov19-269_genomic.fna/target_genomes.txt --output GCA_945903705.1_TH-11nov19-269_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:38:03,845] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:03,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:38:03,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:38:03,867] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:38:03,867] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:38:03,868] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.4718	93	1031	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.4274	91	1031	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.3997	89	1031	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.3783	125	1031	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3471	117	1031	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.1253	103	1031	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.0852	113	1031	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.0776	75	1031	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	76.0434	96	1031	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.0326	127	1031	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.0188	133	1031	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.9872	118	1031	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	75.9386	55	1031	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	75.9343	109	1031	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.8935	103	1031	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	75.8572	101	1031	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.8351	71	1031	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8239	94	1031	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.8072	94	1031	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.8042	105	1031	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	75.7908	103	1031	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	75.7079	81	1031	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	75.6767	52	1031	95	below_threshold
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	75.666	53	1031	95	below_threshold
Pseudorhizobium halotolerans	strain=AB21	GCA_902153235.3	1233081	1233081	type	True	75.5921	51	1031	95	below_threshold
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	75.5642	62	1031	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	75.4921	93	1031	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	75.4615	92	1031	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	75.4252	58	1031	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	75.4252	58	1031	95	below_threshold
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	75.3946	58	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:38:03,870] [INFO] DFAST Taxonomy check result was written to GCA_945903705.1_TH-11nov19-269_genomic.fna/tc_result.tsv
[2023-06-07 23:38:03,871] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:38:03,872] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:38:03,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference/checkm_data
[2023-06-07 23:38:03,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:38:03,915] [INFO] Task started: CheckM
[2023-06-07 23:38:03,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945903705.1_TH-11nov19-269_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945903705.1_TH-11nov19-269_genomic.fna/checkm_input GCA_945903705.1_TH-11nov19-269_genomic.fna/checkm_result
[2023-06-07 23:38:34,108] [INFO] Task succeeded: CheckM
[2023-06-07 23:38:34,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.24%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:38:34,140] [INFO] ===== Completeness check finished =====
[2023-06-07 23:38:34,140] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:38:34,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945903705.1_TH-11nov19-269_genomic.fna/markers.fasta)
[2023-06-07 23:38:34,141] [INFO] Task started: Blastn
[2023-06-07 23:38:34,141] [INFO] Running command: blastn -query GCA_945903705.1_TH-11nov19-269_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5f8d8d-3615-4e70-bfb4-7f8308b3a1e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_945903705.1_TH-11nov19-269_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:38:35,373] [INFO] Task succeeded: Blastn
[2023-06-07 23:38:35,378] [INFO] Selected 24 target genomes.
[2023-06-07 23:38:35,379] [INFO] Target genome list was writen to GCA_945903705.1_TH-11nov19-269_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:38:35,387] [INFO] Task started: fastANI
[2023-06-07 23:38:35,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd34a6e6-e82c-421b-b24a-ff3fffc9921c/GCA_945903705.1_TH-11nov19-269_genomic.fna.gz --refList GCA_945903705.1_TH-11nov19-269_genomic.fna/target_genomes_gtdb.txt --output GCA_945903705.1_TH-11nov19-269_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:38:49,529] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:49,549] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 23:38:49,549] [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_903888485.1	s__SHVO01 sp903888485	78.3773	301	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793085.1	s__GCA-2737725 sp016793085	77.4897	152	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297485.1	s__SCTM01 sp004297485	77.1203	152	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SCTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793005.1	s__GCA-2737725 sp016793005	77.1158	100	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694245.1	s__SHVO01 sp009694245	77.1026	104	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896775.1	s__SHVO01 sp903896775	76.9706	129	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	76.7461	169	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124335.1	s__Tagaea sp016124335	76.5797	57	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869315.1	s__VGEM01 sp016869315	76.5337	119	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__VGEM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	76.4718	93	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693785.1	s__GCA-2737725 sp009693785	76.4149	76	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794025.1	s__Tagaea sp016794025	76.3977	82	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.1754	108	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.1253	103	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.1175	67	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.9965	135	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.9394	110	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	75.9007	81	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCF_008843145.1	s__Skermanella pratensis	75.8072	94	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:38:49,551] [INFO] GTDB search result was written to GCA_945903705.1_TH-11nov19-269_genomic.fna/result_gtdb.tsv
[2023-06-07 23:38:49,552] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:38:49,557] [INFO] DFAST_QC result json was written to GCA_945903705.1_TH-11nov19-269_genomic.fna/dqc_result.json
[2023-06-07 23:38:49,557] [INFO] DFAST_QC completed!
[2023-06-07 23:38:49,557] [INFO] Total running time: 0h1m24s