[2024-01-24 11:26:07,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:07,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:07,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference
[2024-01-24 11:26:08,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:08,760] [INFO] Task started: Prodigal
[2024-01-24 11:26:08,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg49e6d306-b5db-442f-a18b-5b12fef8d597/GCF_008124785.1_ASM812478v1_genomic.fna.gz | prodigal -d GCF_008124785.1_ASM812478v1_genomic.fna/cds.fna -a GCF_008124785.1_ASM812478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:21,515] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:21,516] [INFO] Task started: HMMsearch
[2024-01-24 11:26:21,516] [INFO] Running command: hmmsearch --tblout GCF_008124785.1_ASM812478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference/reference_markers.hmm GCF_008124785.1_ASM812478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:21,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:21,831] [INFO] Found 6/6 markers.
[2024-01-24 11:26:21,860] [INFO] Query marker FASTA was written to GCF_008124785.1_ASM812478v1_genomic.fna/markers.fasta
[2024-01-24 11:26:21,860] [INFO] Task started: Blastn
[2024-01-24 11:26:21,860] [INFO] Running command: blastn -query GCF_008124785.1_ASM812478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference/reference_markers.fasta -out GCF_008124785.1_ASM812478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:22,608] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:22,611] [INFO] Selected 24 target genomes.
[2024-01-24 11:26:22,612] [INFO] Target genome list was writen to GCF_008124785.1_ASM812478v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:22,621] [INFO] Task started: fastANI
[2024-01-24 11:26:22,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e6d306-b5db-442f-a18b-5b12fef8d597/GCF_008124785.1_ASM812478v1_genomic.fna.gz --refList GCF_008124785.1_ASM812478v1_genomic.fna/target_genomes.txt --output GCF_008124785.1_ASM812478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:40,795] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:40,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:40,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:40,814] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:40,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:40,814] [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
Aquimarina intermedia	strain=DSM 17527	GCA_008124785.1	350814	350814	type	True	100.0	1149	1149	95	conclusive
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	77.7774	218	1149	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	77.7761	214	1149	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	77.6354	216	1149	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	77.5332	203	1149	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	77.5281	235	1149	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	77.5218	235	1149	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	77.5108	233	1149	95	below_threshold
Aquimarina pacifica	strain=SW150	GCA_000520955.1	1296415	1296415	type	True	77.4782	191	1149	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	77.4463	222	1149	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	77.4124	213	1149	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	77.3943	231	1149	95	below_threshold
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	77.2449	227	1149	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.2245	74	1149	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.0612	64	1149	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.7352	89	1149	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.7001	90	1149	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.6174	89	1149	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	76.5868	51	1149	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.466	51	1149	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	76.3784	54	1149	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.2366	93	1149	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.023	60	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:40,816] [INFO] DFAST Taxonomy check result was written to GCF_008124785.1_ASM812478v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:40,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:40,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:40,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference/checkm_data
[2024-01-24 11:26:40,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:40,855] [INFO] Task started: CheckM
[2024-01-24 11:26:40,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124785.1_ASM812478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124785.1_ASM812478v1_genomic.fna/checkm_input GCF_008124785.1_ASM812478v1_genomic.fna/checkm_result
[2024-01-24 11:27:21,476] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:21,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,500] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:21,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:21,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124785.1_ASM812478v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:21,501] [INFO] Task started: Blastn
[2024-01-24 11:27:21,501] [INFO] Running command: blastn -query GCF_008124785.1_ASM812478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb54e875-fa99-4198-9719-768a6bcb9fa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124785.1_ASM812478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:22,492] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:22,496] [INFO] Selected 25 target genomes.
[2024-01-24 11:27:22,496] [INFO] Target genome list was writen to GCF_008124785.1_ASM812478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:22,514] [INFO] Task started: fastANI
[2024-01-24 11:27:22,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e6d306-b5db-442f-a18b-5b12fef8d597/GCF_008124785.1_ASM812478v1_genomic.fna.gz --refList GCF_008124785.1_ASM812478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124785.1_ASM812478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:42,314] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:42,339] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:42,340] [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_008124785.1	s__Aquimarina intermedia	100.0	1149	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900299525.1	s__Aquimarina sp900299525	77.7988	217	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008370685.1	s__Aquimarina sp008370685	77.7799	193	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520975.1	s__Aquimarina megaterium	77.7725	219	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_002846555.1	s__Aquimarina sp002846555	77.7644	229	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109375.1	s__Aquimarina amphilecti	77.7611	215	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	77.7382	223	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312745.1	s__Aquimarina sp900312745	77.6881	233	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_900299505.1	s__Aquimarina sp900299505	77.5454	239	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430645.1	s__Aquimarina latercula	77.5273	231	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_003443675.1	s__Aquimarina sp003443675	77.5246	229	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000430665.1	s__Aquimarina muelleri	77.5218	235	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001632745.1	s__Aquimarina aggregata	77.5143	205	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_002895435.1	s__Aquimarina sediminis	77.4463	222	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520995.1	s__Aquimarina macrocephali	77.4124	213	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	77.3943	231	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.2566	74	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006443095.1	s__Aquimarina sp006443095	77.2529	228	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012038135.1	s__Salinimicrobium sp012038135	76.9069	57	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	76.8133	86	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796805.1	s__Algibacter sp009796805	76.7943	97	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	76.7001	90	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004843725.1	s__Olleya sp004843725	76.6875	94	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111075.1	s__Flavobacterium frigoris	76.3784	54	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211785.1	s__Winogradskyella sp004211785	76.0501	70	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:42,342] [INFO] GTDB search result was written to GCF_008124785.1_ASM812478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:42,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:42,349] [INFO] DFAST_QC result json was written to GCF_008124785.1_ASM812478v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:42,349] [INFO] DFAST_QC completed!
[2024-01-24 11:27:42,349] [INFO] Total running time: 0h1m35s