[2024-01-24 11:51:06,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference
[2024-01-24 11:51:07,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:07,955] [INFO] Task started: Prodigal
[2024-01-24 11:51:07,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd4ab13f-9248-482f-861d-e6635dea4e0d/GCF_016735595.1_ASM1673559v1_genomic.fna.gz | prodigal -d GCF_016735595.1_ASM1673559v1_genomic.fna/cds.fna -a GCF_016735595.1_ASM1673559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:01,957] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:01,958] [INFO] Task started: HMMsearch
[2024-01-24 11:52:01,958] [INFO] Running command: hmmsearch --tblout GCF_016735595.1_ASM1673559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference/reference_markers.hmm GCF_016735595.1_ASM1673559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:02,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:02,421] [INFO] Found 6/6 markers.
[2024-01-24 11:52:02,483] [INFO] Query marker FASTA was written to GCF_016735595.1_ASM1673559v1_genomic.fna/markers.fasta
[2024-01-24 11:52:02,483] [INFO] Task started: Blastn
[2024-01-24 11:52:02,483] [INFO] Running command: blastn -query GCF_016735595.1_ASM1673559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference/reference_markers.fasta -out GCF_016735595.1_ASM1673559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:03,079] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:03,084] [INFO] Selected 18 target genomes.
[2024-01-24 11:52:03,085] [INFO] Target genome list was writen to GCF_016735595.1_ASM1673559v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:03,101] [INFO] Task started: fastANI
[2024-01-24 11:52:03,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd4ab13f-9248-482f-861d-e6635dea4e0d/GCF_016735595.1_ASM1673559v1_genomic.fna.gz --refList GCF_016735595.1_ASM1673559v1_genomic.fna/target_genomes.txt --output GCF_016735595.1_ASM1673559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:20,245] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:20,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:20,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:20,257] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:20,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:20,257] [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
Chryseolinea soli	strain=KIS68-18	GCA_003589925.1	2321403	2321403	type	True	80.0752	1142	2625	95	below_threshold
Chryseolinea serpens	strain=DSM 24574	GCA_900129725.1	947013	947013	type	True	79.9897	1164	2625	95	below_threshold
Dawidia soli	strain=PWU37	GCA_018598185.1	2782352	2782352	type	True	77.3364	328	2625	95	below_threshold
Dawidia cretensis	strain=PWU5	GCA_018598175.1	2782350	2782350	type	True	77.1399	283	2625	95	below_threshold
Chryseosolibacter histidini	strain=PWU4	GCA_018598225.1	2782349	2782349	type	True	76.6205	295	2625	95	below_threshold
Pseudochryseolinea flava	strain=SDU1-6	GCA_003286915.1	2059302	2059302	type	True	76.6118	124	2625	95	below_threshold
Ohtaekwangia koreensis	strain=DSM 25262	GCA_900167975.1	688867	688867	type	True	76.2842	140	2625	95	below_threshold
Chryseotalea sanaruensis	strain=Ys	GCA_003990915.1	2482724	2482724	type	True	76.2197	51	2625	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	75.5849	64	2625	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	75.4798	50	2625	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.2562	83	2625	95	below_threshold
Cesiribacter andamanensis	strain=AMV16	GCA_000348925.1	649507	649507	type	True	75.2288	52	2625	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	75.088	57	2625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:20,259] [INFO] DFAST Taxonomy check result was written to GCF_016735595.1_ASM1673559v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:20,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:20,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:20,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference/checkm_data
[2024-01-24 11:52:20,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:20,331] [INFO] Task started: CheckM
[2024-01-24 11:52:20,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016735595.1_ASM1673559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016735595.1_ASM1673559v1_genomic.fna/checkm_input GCF_016735595.1_ASM1673559v1_genomic.fna/checkm_result
[2024-01-24 11:54:44,229] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:44,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:44,258] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:44,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:44,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016735595.1_ASM1673559v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:44,259] [INFO] Task started: Blastn
[2024-01-24 11:54:44,259] [INFO] Running command: blastn -query GCF_016735595.1_ASM1673559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c1eacaf-28da-4913-88f6-51e4fb8764e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_016735595.1_ASM1673559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:45,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:45,100] [INFO] Selected 13 target genomes.
[2024-01-24 11:54:45,100] [INFO] Target genome list was writen to GCF_016735595.1_ASM1673559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:45,111] [INFO] Task started: fastANI
[2024-01-24 11:54:45,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd4ab13f-9248-482f-861d-e6635dea4e0d/GCF_016735595.1_ASM1673559v1_genomic.fna.gz --refList GCF_016735595.1_ASM1673559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016735595.1_ASM1673559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:59,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:59,506] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:59,506] [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_016735595.1	s__Chryseolinea sp016735595	100.0	2625	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003589925.1	s__Chryseolinea soli	80.0803	1141	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129725.1	s__Chryseolinea serpens	79.9919	1163	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598185.1	s__Ohtaekwangia sp018598185	77.3402	329	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598175.1	s__Ohtaekwangia sp018598175	77.1313	284	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598225.1	s__PWU20 sp018598225	76.6217	296	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286915.1	s__Ohtaekwangia flava	76.6118	124	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787565.1	s__JAEUUG01 sp016787565	76.4046	107	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__JAEUUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990915.1	s__Chryseotalea sanaruensis	76.2197	51	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168185.1	s__Ohtaekwangia sp902168185	76.1452	141	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786495.1	s__UBA2336 sp016786495	76.1201	100	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344065.1	s__UBA2336 sp002344065	75.9619	66	2625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	99.89	99.67	0.98	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:59,508] [INFO] GTDB search result was written to GCF_016735595.1_ASM1673559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:59,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:59,514] [INFO] DFAST_QC result json was written to GCF_016735595.1_ASM1673559v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:59,514] [INFO] DFAST_QC completed!
[2024-01-24 11:54:59,514] [INFO] Total running time: 0h3m53s