[2024-01-24 11:51:11,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,411] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference
[2024-01-24 11:51:12,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,667] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe1b0197-4866-47ae-a00d-dff5e232d7a1/GCF_016862755.1_ASM1686275v1_genomic.fna.gz | prodigal -d GCF_016862755.1_ASM1686275v1_genomic.fna/cds.fna -a GCF_016862755.1_ASM1686275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:22,506] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:22,507] [INFO] Task started: HMMsearch
[2024-01-24 11:51:22,507] [INFO] Running command: hmmsearch --tblout GCF_016862755.1_ASM1686275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference/reference_markers.hmm GCF_016862755.1_ASM1686275v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:22,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:22,799] [INFO] Found 6/6 markers.
[2024-01-24 11:51:22,838] [INFO] Query marker FASTA was written to GCF_016862755.1_ASM1686275v1_genomic.fna/markers.fasta
[2024-01-24 11:51:22,839] [INFO] Task started: Blastn
[2024-01-24 11:51:22,839] [INFO] Running command: blastn -query GCF_016862755.1_ASM1686275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference/reference_markers.fasta -out GCF_016862755.1_ASM1686275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:24,327] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:24,334] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:24,334] [INFO] Target genome list was writen to GCF_016862755.1_ASM1686275v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:24,340] [INFO] Task started: fastANI
[2024-01-24 11:51:24,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe1b0197-4866-47ae-a00d-dff5e232d7a1/GCF_016862755.1_ASM1686275v1_genomic.fna.gz --refList GCF_016862755.1_ASM1686275v1_genomic.fna/target_genomes.txt --output GCF_016862755.1_ASM1686275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:42,557] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:42,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:42,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:42,572] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:42,572] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:42,572] [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
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	85.9708	945	1310	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	85.967	974	1310	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	81.8505	802	1310	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	81.6637	770	1310	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	80.7853	662	1310	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.5235	752	1310	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	80.5092	717	1310	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.5068	763	1310	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.4652	687	1310	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.2845	680	1310	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.2449	699	1310	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.1215	703	1310	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	80.0415	683	1310	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.8692	687	1310	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.1894	678	1310	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.1107	616	1310	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	78.8052	613	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:42,575] [INFO] DFAST Taxonomy check result was written to GCF_016862755.1_ASM1686275v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:42,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:42,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:42,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference/checkm_data
[2024-01-24 11:51:42,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:42,624] [INFO] Task started: CheckM
[2024-01-24 11:51:42,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862755.1_ASM1686275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862755.1_ASM1686275v1_genomic.fna/checkm_input GCF_016862755.1_ASM1686275v1_genomic.fna/checkm_result
[2024-01-24 11:52:31,785] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:31,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:31,802] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:31,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:31,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862755.1_ASM1686275v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:31,803] [INFO] Task started: Blastn
[2024-01-24 11:52:31,803] [INFO] Running command: blastn -query GCF_016862755.1_ASM1686275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b42dee6-aad0-48af-9c77-d4348db83336/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862755.1_ASM1686275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:33,958] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:33,963] [INFO] Selected 6 target genomes.
[2024-01-24 11:52:33,963] [INFO] Target genome list was writen to GCF_016862755.1_ASM1686275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:33,967] [INFO] Task started: fastANI
[2024-01-24 11:52:33,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe1b0197-4866-47ae-a00d-dff5e232d7a1/GCF_016862755.1_ASM1686275v1_genomic.fna.gz --refList GCF_016862755.1_ASM1686275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862755.1_ASM1686275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:42,415] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:42,421] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:42,421] [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_016862755.1	s__Cellulomonas pakistanensis	100.0	1304	1310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011603975.1	s__Cellulomonas sp011603975	89.6478	917	1310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	89.6028	1137	1310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_005239125.1	s__Cellulomonas hominis_A	89.2922	936	1310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	89.2391	1136	1310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201095.1	s__Cellulomonas hominis	85.9201	977	1310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:42,423] [INFO] GTDB search result was written to GCF_016862755.1_ASM1686275v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:42,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:42,428] [INFO] DFAST_QC result json was written to GCF_016862755.1_ASM1686275v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:42,428] [INFO] DFAST_QC completed!
[2024-01-24 11:52:42,429] [INFO] Total running time: 0h1m31s