[2024-01-25 19:02:50,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:50,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:50,606] [INFO] DQC Reference Directory: /var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference
[2024-01-25 19:02:51,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:51,748] [INFO] Task started: Prodigal
[2024-01-25 19:02:51,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg761f9bc2-62c2-478b-8a1c-e43ebed7ec17/GCF_003284895.1_ASM328489v1_genomic.fna.gz | prodigal -d GCF_003284895.1_ASM328489v1_genomic.fna/cds.fna -a GCF_003284895.1_ASM328489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:05,798] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:05,799] [INFO] Task started: HMMsearch
[2024-01-25 19:03:05,799] [INFO] Running command: hmmsearch --tblout GCF_003284895.1_ASM328489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference/reference_markers.hmm GCF_003284895.1_ASM328489v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:06,054] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:06,055] [INFO] Found 6/6 markers.
[2024-01-25 19:03:06,088] [INFO] Query marker FASTA was written to GCF_003284895.1_ASM328489v1_genomic.fna/markers.fasta
[2024-01-25 19:03:06,088] [INFO] Task started: Blastn
[2024-01-25 19:03:06,089] [INFO] Running command: blastn -query GCF_003284895.1_ASM328489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference/reference_markers.fasta -out GCF_003284895.1_ASM328489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:06,668] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:06,671] [INFO] Selected 19 target genomes.
[2024-01-25 19:03:06,671] [INFO] Target genome list was writen to GCF_003284895.1_ASM328489v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:06,684] [INFO] Task started: fastANI
[2024-01-25 19:03:06,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg761f9bc2-62c2-478b-8a1c-e43ebed7ec17/GCF_003284895.1_ASM328489v1_genomic.fna.gz --refList GCF_003284895.1_ASM328489v1_genomic.fna/target_genomes.txt --output GCF_003284895.1_ASM328489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:22,428] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:22,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:22,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:22,440] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:03:22,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:22,440] [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
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	100.0	1240	1253	95	conclusive
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	78.5099	463	1253	95	below_threshold
Pontibacter pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	78.4455	459	1253	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	78.444	356	1253	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.3625	416	1253	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	78.1673	419	1253	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	78.1632	363	1253	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.0697	453	1253	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.0658	374	1253	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	78.0479	369	1253	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	77.6764	376	1253	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	77.6269	303	1253	95	below_threshold
Pontibacter akesuensis	strain=AKS 1T	GCA_001611675.1	388950	388950	type	True	77.5979	375	1253	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	77.4958	381	1253	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	77.4176	371	1253	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	77.4037	296	1253	95	below_threshold
Adhaeribacter rhizoryzae	strain=DK36	GCA_008629685.1	2607907	2607907	type	True	76.2162	139	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:22,441] [INFO] DFAST Taxonomy check result was written to GCF_003284895.1_ASM328489v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:22,442] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:22,442] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:22,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference/checkm_data
[2024-01-25 19:03:22,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:22,482] [INFO] Task started: CheckM
[2024-01-25 19:03:22,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003284895.1_ASM328489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003284895.1_ASM328489v1_genomic.fna/checkm_input GCF_003284895.1_ASM328489v1_genomic.fna/checkm_result
[2024-01-25 19:04:02,604] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:02,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:02,625] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:02,625] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:02,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003284895.1_ASM328489v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:02,626] [INFO] Task started: Blastn
[2024-01-25 19:04:02,627] [INFO] Running command: blastn -query GCF_003284895.1_ASM328489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefae1da-9030-4a86-a4b6-3e4994a7b279/dqc_reference/reference_markers_gtdb.fasta -out GCF_003284895.1_ASM328489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:03,438] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:03,449] [INFO] Selected 21 target genomes.
[2024-01-25 19:04:03,449] [INFO] Target genome list was writen to GCF_003284895.1_ASM328489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:03,473] [INFO] Task started: fastANI
[2024-01-25 19:04:03,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg761f9bc2-62c2-478b-8a1c-e43ebed7ec17/GCF_003284895.1_ASM328489v1_genomic.fna.gz --refList GCF_003284895.1_ASM328489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003284895.1_ASM328489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:21,199] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:21,211] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:21,212] [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_003284895.1	s__Pontibacter sp003284895	100.0	1243	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010119545.1	s__Pontibacter fetidus	78.5192	463	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010092985.1	s__Pontibacter pudoricolor	78.4837	460	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003585765.1	s__Pontibacter actiniarum	78.4023	357	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014212495.1	s__Pontibacter sp014212495	78.3965	445	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122615.1	s__Pontibacter sp018122615	78.2484	437	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010686685.1	s__Pontibacter burrus	78.1674	419	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096355.1	s__Pontibacter virosus	78.0796	316	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385705.1	s__Pontibacter sp006385705	78.0568	375	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306105.1	s__Pontibacter sp014306105	78.0472	369	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576375.1	s__Pontibacter oryzae	77.6836	375	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156415.1	s__Pontibacter lucknowensis	77.6604	324	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	98.51	98.51	0.92	0.92	2	-
GCF_014638845.1	s__Pontibacter amylolyticus	77.6366	315	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846395.1	s__Pontibacter ramchanderi	77.6196	305	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	77.6051	375	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015694705.1	s__Pontibacter sp015694705	77.4871	362	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	77.4639	385	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014332515.1	s__Botryobacter beigongshangensis	77.3145	288	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931655.1	s__Pontibacter russatus	77.3057	263	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629685.1	s__Adhaeribacter rhizoryzae	76.2162	139	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:21,213] [INFO] GTDB search result was written to GCF_003284895.1_ASM328489v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:21,214] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:21,217] [INFO] DFAST_QC result json was written to GCF_003284895.1_ASM328489v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:21,217] [INFO] DFAST_QC completed!
[2024-01-25 19:04:21,217] [INFO] Total running time: 0h1m31s