[2023-07-01 02:32:45,853] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:32:45,856] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:32:45,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference
[2023-07-01 02:32:48,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:32:48,185] [INFO] Task started: Prodigal
[2023-07-01 02:32:48,185] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2e2ba6a-9eee-4bef-963a-254a8ab06a5f/GCA_024281145.1_ASM2428114v1_genomic.fna.gz | prodigal -d GCA_024281145.1_ASM2428114v1_genomic.fna/cds.fna -a GCA_024281145.1_ASM2428114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:33:00,978] [INFO] Task succeeded: Prodigal
[2023-07-01 02:33:00,979] [INFO] Task started: HMMsearch
[2023-07-01 02:33:00,979] [INFO] Running command: hmmsearch --tblout GCA_024281145.1_ASM2428114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference/reference_markers.hmm GCA_024281145.1_ASM2428114v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:33:01,255] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:33:01,256] [INFO] Found 6/6 markers.
[2023-07-01 02:33:01,298] [INFO] Query marker FASTA was written to GCA_024281145.1_ASM2428114v1_genomic.fna/markers.fasta
[2023-07-01 02:33:01,298] [INFO] Task started: Blastn
[2023-07-01 02:33:01,299] [INFO] Running command: blastn -query GCA_024281145.1_ASM2428114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference/reference_markers.fasta -out GCA_024281145.1_ASM2428114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:33:02,085] [INFO] Task succeeded: Blastn
[2023-07-01 02:33:02,090] [INFO] Selected 24 target genomes.
[2023-07-01 02:33:02,091] [INFO] Target genome list was writen to GCA_024281145.1_ASM2428114v1_genomic.fna/target_genomes.txt
[2023-07-01 02:33:02,094] [INFO] Task started: fastANI
[2023-07-01 02:33:02,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2e2ba6a-9eee-4bef-963a-254a8ab06a5f/GCA_024281145.1_ASM2428114v1_genomic.fna.gz --refList GCA_024281145.1_ASM2428114v1_genomic.fna/target_genomes.txt --output GCA_024281145.1_ASM2428114v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:33:18,587] [INFO] Task succeeded: fastANI
[2023-07-01 02:33:18,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:33:18,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:33:18,608] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:33:18,609] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:33:18,609] [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	76.9151	159	1285	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	76.5797	135	1285	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	76.4851	105	1285	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.3533	126	1285	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	76.3364	66	1285	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	76.3324	87	1285	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	76.3277	86	1285	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	76.2166	69	1285	95	below_threshold
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	76.1158	64	1285	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.1147	136	1285	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.0728	109	1285	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	76.0607	120	1285	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	76.048	121	1285	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	76.0091	113	1285	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.0088	117	1285	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	76.0022	91	1285	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.9163	157	1285	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8929	165	1285	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.8404	100	1285	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	75.8199	111	1285	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	75.7974	91	1285	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	75.773	93	1285	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:33:18,611] [INFO] DFAST Taxonomy check result was written to GCA_024281145.1_ASM2428114v1_genomic.fna/tc_result.tsv
[2023-07-01 02:33:18,612] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:33:18,612] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:33:18,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference/checkm_data
[2023-07-01 02:33:18,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:33:18,662] [INFO] Task started: CheckM
[2023-07-01 02:33:18,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024281145.1_ASM2428114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024281145.1_ASM2428114v1_genomic.fna/checkm_input GCA_024281145.1_ASM2428114v1_genomic.fna/checkm_result
[2023-07-01 02:33:58,245] [INFO] Task succeeded: CheckM
[2023-07-01 02:33:58,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 02:33:58,270] [INFO] ===== Completeness check finished =====
[2023-07-01 02:33:58,271] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:33:58,271] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024281145.1_ASM2428114v1_genomic.fna/markers.fasta)
[2023-07-01 02:33:58,271] [INFO] Task started: Blastn
[2023-07-01 02:33:58,275] [INFO] Running command: blastn -query GCA_024281145.1_ASM2428114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad69ee8b-6134-4f99-90c6-35a13e427e19/dqc_reference/reference_markers_gtdb.fasta -out GCA_024281145.1_ASM2428114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:33:59,636] [INFO] Task succeeded: Blastn
[2023-07-01 02:33:59,642] [INFO] Selected 13 target genomes.
[2023-07-01 02:33:59,643] [INFO] Target genome list was writen to GCA_024281145.1_ASM2428114v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:33:59,649] [INFO] Task started: fastANI
[2023-07-01 02:33:59,649] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2e2ba6a-9eee-4bef-963a-254a8ab06a5f/GCA_024281145.1_ASM2428114v1_genomic.fna.gz --refList GCA_024281145.1_ASM2428114v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024281145.1_ASM2428114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:34:08,537] [INFO] Task succeeded: fastANI
[2023-07-01 02:34:08,550] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 02:34:08,550] [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_011046675.1	s__AWTP1-13 sp011046675	78.9276	531	1285	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_008933705.1	s__AWTP1-13 sp008933705	77.8989	358	1285	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_017353825.1	s__AWTP1-13 sp017353825	77.4114	232	1285	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_003963125.1	s__AWTP1-13 sp003963125	77.3648	298	1285	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_902826255.1	s__AWTP1-13 sp902826255	77.2156	268	1285	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_011330955.1	s__DSSY01 sp011330955	77.0408	160	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__DSSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	76.828	181	1285	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_017304275.1	s__Hyphomicrobium sp017304275	76.6703	99	1285	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	76.5067	114	1285	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	76.4618	89	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000503895.1	s__Hyphomicrobium nitrativorans	76.4481	107	1285	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	76.1549	161	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	75.9987	123	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:34:08,552] [INFO] GTDB search result was written to GCA_024281145.1_ASM2428114v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:34:08,553] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:34:08,558] [INFO] DFAST_QC result json was written to GCA_024281145.1_ASM2428114v1_genomic.fna/dqc_result.json
[2023-07-01 02:34:08,558] [INFO] DFAST_QC completed!
[2023-07-01 02:34:08,558] [INFO] Total running time: 0h1m23s