[2024-01-24 14:19:15,355] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference
[2024-01-24 14:19:16,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,595] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgd387caa3-01c5-4273-b58b-1c02e1e29f81/GCF_021728535.1_ASM2172853v1_genomic.fna.gz | prodigal -d GCF_021728535.1_ASM2172853v1_genomic.fna/cds.fna -a GCF_021728535.1_ASM2172853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:26,998] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:26,998] [INFO] Task started: HMMsearch
[2024-01-24 14:19:26,999] [INFO] Running command: hmmsearch --tblout GCF_021728535.1_ASM2172853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference/reference_markers.hmm GCF_021728535.1_ASM2172853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:27,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:27,287] [INFO] Found 6/6 markers.
[2024-01-24 14:19:27,324] [INFO] Query marker FASTA was written to GCF_021728535.1_ASM2172853v1_genomic.fna/markers.fasta
[2024-01-24 14:19:27,325] [INFO] Task started: Blastn
[2024-01-24 14:19:27,325] [INFO] Running command: blastn -query GCF_021728535.1_ASM2172853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference/reference_markers.fasta -out GCF_021728535.1_ASM2172853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:28,017] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:28,021] [INFO] Selected 18 target genomes.
[2024-01-24 14:19:28,021] [INFO] Target genome list was writen to GCF_021728535.1_ASM2172853v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:28,031] [INFO] Task started: fastANI
[2024-01-24 14:19:28,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgd387caa3-01c5-4273-b58b-1c02e1e29f81/GCF_021728535.1_ASM2172853v1_genomic.fna.gz --refList GCF_021728535.1_ASM2172853v1_genomic.fna/target_genomes.txt --output GCF_021728535.1_ASM2172853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:42,346] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:42,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:42,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:42,365] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:42,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:42,365] [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
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	79.3916	507	1145	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.8731	445	1145	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.871	443	1145	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.8597	444	1145	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.7591	472	1145	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.7225	439	1145	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.5353	415	1145	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.4688	449	1145	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.3277	407	1145	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.2631	400	1145	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.2541	436	1145	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.204	444	1145	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.1981	383	1145	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	78.1732	330	1145	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.8226	346	1145	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6221	252	1145	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.5985	275	1145	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.2539	264	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:42,367] [INFO] DFAST Taxonomy check result was written to GCF_021728535.1_ASM2172853v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:42,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:42,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:42,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference/checkm_data
[2024-01-24 14:19:42,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:42,413] [INFO] Task started: CheckM
[2024-01-24 14:19:42,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021728535.1_ASM2172853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021728535.1_ASM2172853v1_genomic.fna/checkm_input GCF_021728535.1_ASM2172853v1_genomic.fna/checkm_result
[2024-01-24 14:20:24,573] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:24,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:24,595] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:24,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:24,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021728535.1_ASM2172853v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:24,596] [INFO] Task started: Blastn
[2024-01-24 14:20:24,596] [INFO] Running command: blastn -query GCF_021728535.1_ASM2172853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac088bd-dfd0-4f33-bcbb-b4b46061420a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021728535.1_ASM2172853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,625] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,629] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:25,629] [INFO] Target genome list was writen to GCF_021728535.1_ASM2172853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:25,645] [INFO] Task started: fastANI
[2024-01-24 14:20:25,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgd387caa3-01c5-4273-b58b-1c02e1e29f81/GCF_021728535.1_ASM2172853v1_genomic.fna.gz --refList GCF_021728535.1_ASM2172853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021728535.1_ASM2172853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:35,568] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:35,584] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:20:35,584] [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_000789235.1	s__Wocania ichthyoenteri	82.9867	739	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	81.4807	701	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	79.5208	513	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	79.3826	508	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.8988	440	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.765	471	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.5567	476	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	78.5353	405	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498295.1	s__Wocania sp009498295	78.4888	406	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.2365	438	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	78.2329	410	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	78.2105	383	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	78.1744	313	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	77.802	323	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:35,586] [INFO] GTDB search result was written to GCF_021728535.1_ASM2172853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:35,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:35,590] [INFO] DFAST_QC result json was written to GCF_021728535.1_ASM2172853v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:35,591] [INFO] DFAST_QC completed!
[2024-01-24 14:20:35,591] [INFO] Total running time: 0h1m20s