[2024-01-24 14:05:53,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference
[2024-01-24 14:05:55,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,041] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,041] [INFO] Running command: gunzip -c /var/lib/cwl/stgc107f43c-8f38-4132-be30-a47cf9d23a03/GCF_004116345.1_ASM411634v1_genomic.fna.gz | prodigal -d GCF_004116345.1_ASM411634v1_genomic.fna/cds.fna -a GCF_004116345.1_ASM411634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:00,299] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:00,300] [INFO] Task started: HMMsearch
[2024-01-24 14:06:00,300] [INFO] Running command: hmmsearch --tblout GCF_004116345.1_ASM411634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference/reference_markers.hmm GCF_004116345.1_ASM411634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:00,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:00,625] [INFO] Found 6/6 markers.
[2024-01-24 14:06:00,654] [INFO] Query marker FASTA was written to GCF_004116345.1_ASM411634v1_genomic.fna/markers.fasta
[2024-01-24 14:06:00,655] [INFO] Task started: Blastn
[2024-01-24 14:06:00,655] [INFO] Running command: blastn -query GCF_004116345.1_ASM411634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference/reference_markers.fasta -out GCF_004116345.1_ASM411634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:01,336] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:01,340] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:01,340] [INFO] Target genome list was writen to GCF_004116345.1_ASM411634v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:01,767] [INFO] Task started: fastANI
[2024-01-24 14:06:01,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgc107f43c-8f38-4132-be30-a47cf9d23a03/GCF_004116345.1_ASM411634v1_genomic.fna.gz --refList GCF_004116345.1_ASM411634v1_genomic.fna/target_genomes.txt --output GCF_004116345.1_ASM411634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:08,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:08,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:08,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:08,582] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:08,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:08,582] [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
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	100.0	973	973	95	conclusive
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	100.0	972	973	95	conclusive
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	80.2068	584	973	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	80.1655	599	973	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	79.1401	430	973	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	78.9116	405	973	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	78.8978	415	973	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	78.4054	357	973	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	78.0714	367	973	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	77.9814	290	973	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	77.4683	237	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:08,584] [INFO] DFAST Taxonomy check result was written to GCF_004116345.1_ASM411634v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:08,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:08,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:08,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference/checkm_data
[2024-01-24 14:06:08,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:08,633] [INFO] Task started: CheckM
[2024-01-24 14:06:08,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116345.1_ASM411634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116345.1_ASM411634v1_genomic.fna/checkm_input GCF_004116345.1_ASM411634v1_genomic.fna/checkm_result
[2024-01-24 14:06:32,286] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:32,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,310] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:32,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:32,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116345.1_ASM411634v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:32,311] [INFO] Task started: Blastn
[2024-01-24 14:06:32,312] [INFO] Running command: blastn -query GCF_004116345.1_ASM411634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbafffb90-9504-41fb-9419-d5ec2fb26ab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116345.1_ASM411634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:33,235] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:33,238] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:33,239] [INFO] Target genome list was writen to GCF_004116345.1_ASM411634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:33,269] [INFO] Task started: fastANI
[2024-01-24 14:06:33,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgc107f43c-8f38-4132-be30-a47cf9d23a03/GCF_004116345.1_ASM411634v1_genomic.fna.gz --refList GCF_004116345.1_ASM411634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116345.1_ASM411634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:43,172] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:43,188] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:43,188] [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_006459125.1	s__Halarcobacter anaerophilus	100.0	972	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.86	97.73	0.95	0.89	3	conclusive
GCF_013201825.1	s__Halarcobacter ebronensis	80.1423	601	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCA_003252105.1	s__Halarcobacter sp003252105	79.2259	410	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771535.1	s__Halarcobacter arenosus	79.1079	433	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116625.1	s__Halarcobacter mediterraneus	79.0786	438	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346815.1	s__Halarcobacter bivalviorum	78.9178	413	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCA_001895145.1	s__Halarcobacter sp001895145	78.8802	410	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116455.1	s__Halarcobacter sp004116455	78.8377	371	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCA_004118855.1	s__Halarcobacter sp004118855	78.745	407	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	78.7183	384	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	78.5973	445	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116725.1	s__Malaciobacter sp004116725	78.4062	365	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544935.1	s__Malaciobacter molluscorum	78.3746	361	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCF_013201725.1	s__Aliarcobacter defluvii	78.1106	357	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_003544915.1	s__Aliarcobacter ellisii	78.0414	343	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_004299785.2	s__Aliarcobacter porcinus	77.4467	238	973	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:43,191] [INFO] GTDB search result was written to GCF_004116345.1_ASM411634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:43,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:43,200] [INFO] DFAST_QC result json was written to GCF_004116345.1_ASM411634v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:43,200] [INFO] DFAST_QC completed!
[2024-01-24 14:06:43,200] [INFO] Total running time: 0h0m50s