[2023-06-08 03:59:55,818] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:59:55,820] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:59:55,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference
[2023-06-08 03:59:57,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:59:57,187] [INFO] Task started: Prodigal
[2023-06-08 03:59:57,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg29c2b09b-5f53-43aa-90c7-2226e3ddbcde/GCA_945862355.1_MH-08apr19-168_genomic.fna.gz | prodigal -d GCA_945862355.1_MH-08apr19-168_genomic.fna/cds.fna -a GCA_945862355.1_MH-08apr19-168_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:00:10,861] [INFO] Task succeeded: Prodigal
[2023-06-08 04:00:10,862] [INFO] Task started: HMMsearch
[2023-06-08 04:00:10,862] [INFO] Running command: hmmsearch --tblout GCA_945862355.1_MH-08apr19-168_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference/reference_markers.hmm GCA_945862355.1_MH-08apr19-168_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:00:11,174] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:00:11,175] [INFO] Found 6/6 markers.
[2023-06-08 04:00:11,222] [INFO] Query marker FASTA was written to GCA_945862355.1_MH-08apr19-168_genomic.fna/markers.fasta
[2023-06-08 04:00:11,223] [INFO] Task started: Blastn
[2023-06-08 04:00:11,223] [INFO] Running command: blastn -query GCA_945862355.1_MH-08apr19-168_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference/reference_markers.fasta -out GCA_945862355.1_MH-08apr19-168_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:00:12,113] [INFO] Task succeeded: Blastn
[2023-06-08 04:00:12,117] [INFO] Selected 30 target genomes.
[2023-06-08 04:00:12,117] [INFO] Target genome list was writen to GCA_945862355.1_MH-08apr19-168_genomic.fna/target_genomes.txt
[2023-06-08 04:00:12,138] [INFO] Task started: fastANI
[2023-06-08 04:00:12,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c2b09b-5f53-43aa-90c7-2226e3ddbcde/GCA_945862355.1_MH-08apr19-168_genomic.fna.gz --refList GCA_945862355.1_MH-08apr19-168_genomic.fna/target_genomes.txt --output GCA_945862355.1_MH-08apr19-168_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:00:33,403] [INFO] Task succeeded: fastANI
[2023-06-08 04:00:33,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:00:33,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:00:33,432] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:00:33,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:00:33,432] [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
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.6077	199	1521	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.0942	160	1521	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	76.8326	196	1521	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.7321	181	1521	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.6211	209	1521	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.6192	182	1521	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.5662	203	1521	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	76.5344	122	1521	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	76.5195	145	1521	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	76.4915	147	1521	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.4518	165	1521	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	76.4401	145	1521	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.4365	150	1521	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.4279	165	1521	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.3806	140	1521	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.3335	163	1521	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	76.2831	140	1521	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	76.2762	126	1521	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.227	213	1521	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.206	148	1521	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.2027	167	1521	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	76.1711	108	1521	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.1647	148	1521	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	76.1079	140	1521	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.0418	97	1521	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.9938	116	1521	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	75.7971	86	1521	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	75.7971	86	1521	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	75.7839	87	1521	95	below_threshold
Neomegalonema perideroedes	strain=DSM 15528	GCA_000374145.1	217219	217219	type	True	75.3555	58	1521	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:00:33,434] [INFO] DFAST Taxonomy check result was written to GCA_945862355.1_MH-08apr19-168_genomic.fna/tc_result.tsv
[2023-06-08 04:00:33,435] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:00:33,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:00:33,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference/checkm_data
[2023-06-08 04:00:33,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:00:33,483] [INFO] Task started: CheckM
[2023-06-08 04:00:33,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945862355.1_MH-08apr19-168_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945862355.1_MH-08apr19-168_genomic.fna/checkm_input GCA_945862355.1_MH-08apr19-168_genomic.fna/checkm_result
[2023-06-08 04:01:14,705] [INFO] Task succeeded: CheckM
[2023-06-08 04:01:14,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:01:14,730] [INFO] ===== Completeness check finished =====
[2023-06-08 04:01:14,731] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:01:14,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945862355.1_MH-08apr19-168_genomic.fna/markers.fasta)
[2023-06-08 04:01:14,731] [INFO] Task started: Blastn
[2023-06-08 04:01:14,732] [INFO] Running command: blastn -query GCA_945862355.1_MH-08apr19-168_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a1348f8-2550-4936-b354-f3f5d65f062f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945862355.1_MH-08apr19-168_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:01:16,366] [INFO] Task succeeded: Blastn
[2023-06-08 04:01:16,371] [INFO] Selected 27 target genomes.
[2023-06-08 04:01:16,371] [INFO] Target genome list was writen to GCA_945862355.1_MH-08apr19-168_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:01:16,419] [INFO] Task started: fastANI
[2023-06-08 04:01:16,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c2b09b-5f53-43aa-90c7-2226e3ddbcde/GCA_945862355.1_MH-08apr19-168_genomic.fna.gz --refList GCA_945862355.1_MH-08apr19-168_genomic.fna/target_genomes_gtdb.txt --output GCA_945862355.1_MH-08apr19-168_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:01:37,345] [INFO] Task succeeded: fastANI
[2023-06-08 04:01:37,371] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 04:01:37,372] [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_009708035.1	s__Hyphomicrobium_A sp009708035	77.6077	199	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	77.2324	161	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330955.1	s__DSSY01 sp011330955	77.136	244	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__DSSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	77.1357	184	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019137195.1	s__Hyphomicrobium sp019137195	77.1123	175	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963125.1	s__AWTP1-13 sp003963125	77.1072	255	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000503895.1	s__Hyphomicrobium nitrativorans	77.0942	160	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464955.1	s__Ga0077555 sp001464955	77.0845	236	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046675.1	s__AWTP1-13 sp011046675	77.003	289	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	76.9713	157	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826715.1	s__CADEFX01 sp902826715	76.8645	166	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__CADEFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	76.8326	196	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	76.8237	164	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242645.1	s__ZC4RG25 sp003242645	76.6702	124	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	76.6574	116	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCA_016793595.1	s__Phreatobacter sp016793595	76.5728	159	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242215.1	s__Hyphomicrobium sp018242215	76.5439	94	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	76.4195	167	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	76.3873	151	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897035.1	s__Methylopila sp002897035	76.3744	148	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002919265.1	s__ZC4RG25 sp002919265	76.3332	125	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	99.72	99.72	0.95	0.95	2	-
GCA_001464755.1	s__Ga0077555 sp001464755	76.258	179	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	76.1802	131	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	76.1692	166	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046735.1	s__Nordella sp011046735	75.9778	117	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911755.1	s__Sphingosinicella sp013911755	75.8405	68	1521	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:01:37,373] [INFO] GTDB search result was written to GCA_945862355.1_MH-08apr19-168_genomic.fna/result_gtdb.tsv
[2023-06-08 04:01:37,374] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:01:37,379] [INFO] DFAST_QC result json was written to GCA_945862355.1_MH-08apr19-168_genomic.fna/dqc_result.json
[2023-06-08 04:01:37,379] [INFO] DFAST_QC completed!
[2023-06-08 04:01:37,379] [INFO] Total running time: 0h1m42s