[2024-01-24 14:05:49,190] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:49,193] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:49,193] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference
[2024-01-24 14:05:50,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,611] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,611] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fe599ba-89f2-4155-83c3-f7f24bff9f7f/GCF_000686045.1_ASM68604v1_genomic.fna.gz | prodigal -d GCF_000686045.1_ASM68604v1_genomic.fna/cds.fna -a GCF_000686045.1_ASM68604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:02,134] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:02,134] [INFO] Task started: HMMsearch
[2024-01-24 14:06:02,134] [INFO] Running command: hmmsearch --tblout GCF_000686045.1_ASM68604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference/reference_markers.hmm GCF_000686045.1_ASM68604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:02,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:02,455] [INFO] Found 6/6 markers.
[2024-01-24 14:06:02,508] [INFO] Query marker FASTA was written to GCF_000686045.1_ASM68604v1_genomic.fna/markers.fasta
[2024-01-24 14:06:02,509] [INFO] Task started: Blastn
[2024-01-24 14:06:02,509] [INFO] Running command: blastn -query GCF_000686045.1_ASM68604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference/reference_markers.fasta -out GCF_000686045.1_ASM68604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:03,358] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:03,363] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:03,363] [INFO] Target genome list was writen to GCF_000686045.1_ASM68604v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:03,372] [INFO] Task started: fastANI
[2024-01-24 14:06:03,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe599ba-89f2-4155-83c3-f7f24bff9f7f/GCF_000686045.1_ASM68604v1_genomic.fna.gz --refList GCF_000686045.1_ASM68604v1_genomic.fna/target_genomes.txt --output GCF_000686045.1_ASM68604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:20,640] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:20,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:20,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:20,654] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:20,655] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:20,655] [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
Fodinicurvata fenggangensis	strain=DSM 21160	GCA_000686045.1	1121830	1121830	type	True	100.0	1234	1242	95	conclusive
Fodinicurvata sediminis	strain=DSM 21159	GCA_000420625.1	1121832	1121832	type	True	87.1292	1017	1242	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.5123	233	1242	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.2257	276	1242	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2041	280	1242	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	77.0688	142	1242	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.0281	132	1242	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.9596	151	1242	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.9588	162	1242	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	76.955	94	1242	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.8968	166	1242	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.7982	151	1242	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.5541	160	1242	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.3348	161	1242	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	76.1624	91	1242	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	76.0745	96	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:20,657] [INFO] DFAST Taxonomy check result was written to GCF_000686045.1_ASM68604v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:20,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:20,658] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:20,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference/checkm_data
[2024-01-24 14:06:20,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:20,700] [INFO] Task started: CheckM
[2024-01-24 14:06:20,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000686045.1_ASM68604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000686045.1_ASM68604v1_genomic.fna/checkm_input GCF_000686045.1_ASM68604v1_genomic.fna/checkm_result
[2024-01-24 14:06:58,752] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:58,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:58,777] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:58,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:58,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000686045.1_ASM68604v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:58,778] [INFO] Task started: Blastn
[2024-01-24 14:06:58,778] [INFO] Running command: blastn -query GCF_000686045.1_ASM68604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3f1a116-d25a-4f20-8df6-ddada0338699/dqc_reference/reference_markers_gtdb.fasta -out GCF_000686045.1_ASM68604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:00,150] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:00,154] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:00,154] [INFO] Target genome list was writen to GCF_000686045.1_ASM68604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:00,184] [INFO] Task started: fastANI
[2024-01-24 14:07:00,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe599ba-89f2-4155-83c3-f7f24bff9f7f/GCF_000686045.1_ASM68604v1_genomic.fna.gz --refList GCF_000686045.1_ASM68604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000686045.1_ASM68604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:17,893] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:17,911] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:17,911] [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_000686045.1	s__Fodinicurvata fenggangensis	100.0	1233	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Fodinicurvata	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420625.1	s__Fodinicurvata sediminis	87.1292	1017	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Fodinicurvata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006969625.1	s__Algihabitans sp006969625	77.5802	242	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	77.5446	233	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.2156	279	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900100455.1	s__Roseospirillum parvum	77.046	131	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	77.0363	203	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	76.8876	175	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	76.7717	156	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	76.6481	181	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.6391	151	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	76.6098	140	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	76.6091	158	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.4497	136	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_013822765.1	s__SYSU-D60009 sp013822765	76.4428	116	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	76.321	160	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.1383	119	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550665.1	s__Rhodobaculum sp003550665	75.7468	61	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.32	99.19	0.86	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:17,913] [INFO] GTDB search result was written to GCF_000686045.1_ASM68604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:17,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:17,917] [INFO] DFAST_QC result json was written to GCF_000686045.1_ASM68604v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:17,917] [INFO] DFAST_QC completed!
[2024-01-24 14:07:17,917] [INFO] Total running time: 0h1m29s