[2024-01-24 10:47:10,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference
[2024-01-24 10:47:12,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,158] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg453dd4c6-b1b0-4d31-aa86-723e010a8e77/GCF_021025975.1_ASM2102597v1_genomic.fna.gz | prodigal -d GCF_021025975.1_ASM2102597v1_genomic.fna/cds.fna -a GCF_021025975.1_ASM2102597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:17,692] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:17,693] [INFO] Task started: HMMsearch
[2024-01-24 10:47:17,693] [INFO] Running command: hmmsearch --tblout GCF_021025975.1_ASM2102597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference/reference_markers.hmm GCF_021025975.1_ASM2102597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:17,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:17,955] [INFO] Found 6/6 markers.
[2024-01-24 10:47:17,975] [INFO] Query marker FASTA was written to GCF_021025975.1_ASM2102597v1_genomic.fna/markers.fasta
[2024-01-24 10:47:17,975] [INFO] Task started: Blastn
[2024-01-24 10:47:17,975] [INFO] Running command: blastn -query GCF_021025975.1_ASM2102597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference/reference_markers.fasta -out GCF_021025975.1_ASM2102597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,652] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,656] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:19,657] [INFO] Target genome list was writen to GCF_021025975.1_ASM2102597v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,450] [INFO] Task started: fastANI
[2024-01-24 10:47:20,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg453dd4c6-b1b0-4d31-aa86-723e010a8e77/GCF_021025975.1_ASM2102597v1_genomic.fna.gz --refList GCF_021025975.1_ASM2102597v1_genomic.fna/target_genomes.txt --output GCF_021025975.1_ASM2102597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:26,507] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:26,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:26,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:26,521] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:47:26,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:26,522] [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
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	100.0	607	607	95	conclusive
Neisseria cinerea	strain=ATCC 14685	GCA_000173895.1	483	483	type	True	99.9766	591	607	95	conclusive
Neisseria cinerea	strain=NCTC10294	GCA_900475315.1	483	483	type	True	96.9647	566	607	95	conclusive
Neisseria cinerea	strain=FDAARGOS_871	GCA_016028715.1	483	483	type	True	96.9179	566	607	95	conclusive
Neisseria lactamica	strain=NCTC10617	GCA_901482445.1	486	486	type	True	90.4286	538	607	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	90.411	519	607	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	86.4637	416	607	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	86.4054	392	607	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	85.8076	400	607	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	85.1105	373	607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:26,524] [INFO] DFAST Taxonomy check result was written to GCF_021025975.1_ASM2102597v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:26,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:26,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:26,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference/checkm_data
[2024-01-24 10:47:26,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:26,546] [INFO] Task started: CheckM
[2024-01-24 10:47:26,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021025975.1_ASM2102597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021025975.1_ASM2102597v1_genomic.fna/checkm_input GCF_021025975.1_ASM2102597v1_genomic.fna/checkm_result
[2024-01-24 10:47:49,060] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:49,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:49,085] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:49,086] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:49,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021025975.1_ASM2102597v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:49,087] [INFO] Task started: Blastn
[2024-01-24 10:47:49,087] [INFO] Running command: blastn -query GCF_021025975.1_ASM2102597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71332b5e-6006-4c7f-a16f-11ac05566a0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_021025975.1_ASM2102597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:50,595] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:50,600] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:50,600] [INFO] Target genome list was writen to GCF_021025975.1_ASM2102597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:50,705] [INFO] Task started: fastANI
[2024-01-24 10:47:50,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg453dd4c6-b1b0-4d31-aa86-723e010a8e77/GCF_021025975.1_ASM2102597v1_genomic.fna.gz --refList GCF_021025975.1_ASM2102597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021025975.1_ASM2102597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:47:58,397] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,409] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:47:58,409] [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_900475315.1	s__Neisseria cinerea	96.9647	566	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.50	96.82	0.94	0.93	8	conclusive
GCF_000176735.1	s__Neisseria polysaccharea	91.5623	504	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.23	95.40	0.91	0.88	7	-
GCF_003044455.1	s__Neisseria bergeri	91.1523	532	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.18	96.14	0.94	0.92	5	-
GCF_000193795.1	s__Neisseria lactamica_A	90.4668	511	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901482445.1	s__Neisseria lactamica	90.4248	538	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.73	97.33	0.93	0.89	36	-
GCF_900638555.1	s__Neisseria meningitidis	90.3413	522	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	97.78	97.16	0.95	0.86	2138	-
GCF_003315235.1	s__Neisseria gonorrhoeae	89.8887	510	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	99.56	98.98	0.97	0.89	796	-
GCF_003045025.1	s__Neisseria subflava_A	85.4625	390	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.3115	96.25	95.58	0.94	0.91	14	-
GCF_001618085.1	s__Neisseria flavescens_C	85.4103	378	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_003351665.1	s__Neisseria perflava	85.1689	391	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.77	96.48	0.96	0.95	5	-
GCF_013267835.1	s__Neisseria sp000186165	85.1668	380	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_003044645.1	s__Neisseria subflava_B	85.1383	393	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
GCF_001618065.1	s__Neisseria flavescens_A	84.9426	389	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6469	95.75	95.69	0.92	0.91	4	-
GCF_001618015.1	s__Neisseria flavescens_B	84.8635	396	607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	95.75	95.73	0.88	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,411] [INFO] GTDB search result was written to GCF_021025975.1_ASM2102597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:47:58,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:47:58,415] [INFO] DFAST_QC result json was written to GCF_021025975.1_ASM2102597v1_genomic.fna/dqc_result.json
[2024-01-24 10:47:58,415] [INFO] DFAST_QC completed!
[2024-01-24 10:47:58,415] [INFO] Total running time: 0h0m48s