[2024-01-25 17:53:50,445] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference
[2024-01-25 17:53:51,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,617] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg038c1f56-2bb3-4abc-88e1-a0297f3cc0f2/GCF_009708035.1_ASM970803v1_genomic.fna.gz | prodigal -d GCF_009708035.1_ASM970803v1_genomic.fna/cds.fna -a GCF_009708035.1_ASM970803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:02,584] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:02,585] [INFO] Task started: HMMsearch
[2024-01-25 17:54:02,585] [INFO] Running command: hmmsearch --tblout GCF_009708035.1_ASM970803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference/reference_markers.hmm GCF_009708035.1_ASM970803v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:02,808] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:02,810] [INFO] Found 6/6 markers.
[2024-01-25 17:54:02,843] [INFO] Query marker FASTA was written to GCF_009708035.1_ASM970803v1_genomic.fna/markers.fasta
[2024-01-25 17:54:02,843] [INFO] Task started: Blastn
[2024-01-25 17:54:02,843] [INFO] Running command: blastn -query GCF_009708035.1_ASM970803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference/reference_markers.fasta -out GCF_009708035.1_ASM970803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:03,714] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:03,718] [INFO] Selected 21 target genomes.
[2024-01-25 17:54:03,718] [INFO] Target genome list was writen to GCF_009708035.1_ASM970803v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:03,757] [INFO] Task started: fastANI
[2024-01-25 17:54:03,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg038c1f56-2bb3-4abc-88e1-a0297f3cc0f2/GCF_009708035.1_ASM970803v1_genomic.fna.gz --refList GCF_009708035.1_ASM970803v1_genomic.fna/target_genomes.txt --output GCF_009708035.1_ASM970803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:21,553] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:21,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:21,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:21,566] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:21,566] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:21,567] [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	100.0	1301	1301	95	conclusive
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	79.061	529	1301	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	79.0186	537	1301	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	78.3669	392	1301	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	78.2553	335	1301	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	77.8763	274	1301	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.741	221	1301	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	77.7305	260	1301	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.4789	305	1301	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.4378	243	1301	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.3775	282	1301	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.377	251	1301	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.3363	245	1301	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	77.1845	236	1301	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.1295	124	1301	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	77.106	133	1301	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.9158	194	1301	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.8471	254	1301	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	76.774	269	1301	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	76.5878	169	1301	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3929	250	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:21,568] [INFO] DFAST Taxonomy check result was written to GCF_009708035.1_ASM970803v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:21,568] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:21,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:21,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference/checkm_data
[2024-01-25 17:54:21,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:21,609] [INFO] Task started: CheckM
[2024-01-25 17:54:21,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009708035.1_ASM970803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009708035.1_ASM970803v1_genomic.fna/checkm_input GCF_009708035.1_ASM970803v1_genomic.fna/checkm_result
[2024-01-25 17:54:54,212] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:54,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:54,234] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:54,234] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:54,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009708035.1_ASM970803v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:54,235] [INFO] Task started: Blastn
[2024-01-25 17:54:54,235] [INFO] Running command: blastn -query GCF_009708035.1_ASM970803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6509da-85d5-4791-aba7-150a9682816d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009708035.1_ASM970803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:56,051] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:56,054] [INFO] Selected 12 target genomes.
[2024-01-25 17:54:56,055] [INFO] Target genome list was writen to GCF_009708035.1_ASM970803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:56,065] [INFO] Task started: fastANI
[2024-01-25 17:54:56,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg038c1f56-2bb3-4abc-88e1-a0297f3cc0f2/GCF_009708035.1_ASM970803v1_genomic.fna.gz --refList GCF_009708035.1_ASM970803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009708035.1_ASM970803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:06,679] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:06,687] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:55:06,687] [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	100.0	1301	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	83.8254	861	1301	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	80.8315	742	1301	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_013306565.1	s__Hyphomicrobium_A sulfonivorans	79.0389	527	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	98.55	97.10	0.95	0.91	3	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	78.6282	302	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	78.4366	378	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	78.3764	391	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCA_008933705.1	s__AWTP1-13 sp008933705	78.3516	331	1301	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	78.1255	327	1301	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_902826555.1	s__Hyphomicrobium sp902826555	78.0062	391	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117415.1	s__Ga0077555 sp900117415	77.8228	278	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	97.09	97.07	0.95	0.91	3	-
GCA_005502805.1	s__Bosea sp005502805	77.0735	235	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:06,689] [INFO] GTDB search result was written to GCF_009708035.1_ASM970803v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:06,690] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:06,693] [INFO] DFAST_QC result json was written to GCF_009708035.1_ASM970803v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:06,693] [INFO] DFAST_QC completed!
[2024-01-25 17:55:06,693] [INFO] Total running time: 0h1m16s