[2024-01-24 13:49:27,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference
[2024-01-24 13:49:28,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,907] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2dbe281-120f-46a1-914a-e96b0e7b664e/GCF_003933245.1_ASM393324v1_genomic.fna.gz | prodigal -d GCF_003933245.1_ASM393324v1_genomic.fna/cds.fna -a GCF_003933245.1_ASM393324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,914] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,915] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,915] [INFO] Running command: hmmsearch --tblout GCF_003933245.1_ASM393324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference/reference_markers.hmm GCF_003933245.1_ASM393324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:50,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:50,251] [INFO] Found 6/6 markers.
[2024-01-24 13:49:50,287] [INFO] Query marker FASTA was written to GCF_003933245.1_ASM393324v1_genomic.fna/markers.fasta
[2024-01-24 13:49:50,287] [INFO] Task started: Blastn
[2024-01-24 13:49:50,287] [INFO] Running command: blastn -query GCF_003933245.1_ASM393324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference/reference_markers.fasta -out GCF_003933245.1_ASM393324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,928] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:50,929] [INFO] Target genome list was writen to GCF_003933245.1_ASM393324v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,939] [INFO] Task started: fastANI
[2024-01-24 13:49:50,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2dbe281-120f-46a1-914a-e96b0e7b664e/GCF_003933245.1_ASM393324v1_genomic.fna.gz --refList GCF_003933245.1_ASM393324v1_genomic.fna/target_genomes.txt --output GCF_003933245.1_ASM393324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:02,577] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:02,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:02,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:02,591] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:02,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:02,591] [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
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	100.0	1369	1370	95	conclusive
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	85.0284	978	1370	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	84.8429	1015	1370	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	82.5634	815	1370	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	82.4623	823	1370	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.6302	336	1370	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	77.0142	197	1370	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.5674	132	1370	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	76.5019	129	1370	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.2389	92	1370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:02,593] [INFO] DFAST Taxonomy check result was written to GCF_003933245.1_ASM393324v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:02,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:02,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:02,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference/checkm_data
[2024-01-24 13:50:02,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:02,643] [INFO] Task started: CheckM
[2024-01-24 13:50:02,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003933245.1_ASM393324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003933245.1_ASM393324v1_genomic.fna/checkm_input GCF_003933245.1_ASM393324v1_genomic.fna/checkm_result
[2024-01-24 13:51:02,044] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:02,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:02,064] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:02,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:02,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003933245.1_ASM393324v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:02,066] [INFO] Task started: Blastn
[2024-01-24 13:51:02,066] [INFO] Running command: blastn -query GCF_003933245.1_ASM393324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaf74d07-e61c-4b9e-93e7-c012e98d9a27/dqc_reference/reference_markers_gtdb.fasta -out GCF_003933245.1_ASM393324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:02,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:02,894] [INFO] Selected 13 target genomes.
[2024-01-24 13:51:02,895] [INFO] Target genome list was writen to GCF_003933245.1_ASM393324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:02,905] [INFO] Task started: fastANI
[2024-01-24 13:51:02,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2dbe281-120f-46a1-914a-e96b0e7b664e/GCF_003933245.1_ASM393324v1_genomic.fna.gz --refList GCF_003933245.1_ASM393324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003933245.1_ASM393324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:13,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:13,126] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:13,126] [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_003933245.1	s__Maribacter algicola	100.0	1369	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002742265.1	s__Maribacter sp002742265	90.458	1065	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	84.8368	1016	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_002269385.1	s__Maribacter cobaltidurans	82.5534	816	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018100785.1	s__Maribacter sp018100785	77.942	311	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	77.6488	334	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	77.0228	179	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	77.0142	197	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.6517	144	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306415.1	s__Croceitalea dokdonensis	76.5674	132	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.3745	115	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.285	62	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626755.1	s__Ulvibacterium marinum	76.2623	168	1370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,128] [INFO] GTDB search result was written to GCF_003933245.1_ASM393324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:13,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:13,132] [INFO] DFAST_QC result json was written to GCF_003933245.1_ASM393324v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:13,132] [INFO] DFAST_QC completed!
[2024-01-24 13:51:13,132] [INFO] Total running time: 0h1m46s