[2024-01-24 13:45:46,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference
[2024-01-24 13:45:47,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,530] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,530] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaa50215-a013-4591-8c8b-1a6715b32b84/GCF_008151785.1_ASM815178v1_genomic.fna.gz | prodigal -d GCF_008151785.1_ASM815178v1_genomic.fna/cds.fna -a GCF_008151785.1_ASM815178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:51,970] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:51,971] [INFO] Task started: HMMsearch
[2024-01-24 13:45:51,971] [INFO] Running command: hmmsearch --tblout GCF_008151785.1_ASM815178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference/reference_markers.hmm GCF_008151785.1_ASM815178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:52,280] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:52,281] [INFO] Found 6/6 markers.
[2024-01-24 13:45:52,304] [INFO] Query marker FASTA was written to GCF_008151785.1_ASM815178v1_genomic.fna/markers.fasta
[2024-01-24 13:45:52,304] [INFO] Task started: Blastn
[2024-01-24 13:45:52,305] [INFO] Running command: blastn -query GCF_008151785.1_ASM815178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference/reference_markers.fasta -out GCF_008151785.1_ASM815178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:52,902] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:52,905] [INFO] Selected 11 target genomes.
[2024-01-24 13:45:52,905] [INFO] Target genome list was writen to GCF_008151785.1_ASM815178v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:52,945] [INFO] Task started: fastANI
[2024-01-24 13:45:52,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa50215-a013-4591-8c8b-1a6715b32b84/GCF_008151785.1_ASM815178v1_genomic.fna.gz --refList GCF_008151785.1_ASM815178v1_genomic.fna/target_genomes.txt --output GCF_008151785.1_ASM815178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:45:59,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:59,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:45:59,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:45:59,373] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:45:59,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:45:59,374] [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
Peptacetobacter hiranonis	strain=DSM 13275	GCA_008151785.1	89152	89152	type	True	100.0	837	840	95	conclusive
Peptacetobacter hiranonis	strain=DSM 13275	GCA_000156055.1	89152	89152	type	True	99.7957	799	840	95	conclusive
Peptacetobacter hominis	strain=ZHW00191	GCA_006861675.1	2743610	2743610	type	True	80.3527	322	840	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	79.0579	151	840	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	78.9515	179	840	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_000154445.1	261299	261299	type	True	78.6658	162	840	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	78.1092	135	840	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_900167285.1	261299	261299	type	True	78.0253	162	840	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	77.8285	149	840	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	77.1285	166	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:45:59,375] [INFO] DFAST Taxonomy check result was written to GCF_008151785.1_ASM815178v1_genomic.fna/tc_result.tsv
[2024-01-24 13:45:59,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:45:59,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:45:59,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference/checkm_data
[2024-01-24 13:45:59,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:45:59,403] [INFO] Task started: CheckM
[2024-01-24 13:45:59,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008151785.1_ASM815178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008151785.1_ASM815178v1_genomic.fna/checkm_input GCF_008151785.1_ASM815178v1_genomic.fna/checkm_result
[2024-01-24 13:46:21,044] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:21,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:21,066] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:21,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:21,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008151785.1_ASM815178v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:21,067] [INFO] Task started: Blastn
[2024-01-24 13:46:21,067] [INFO] Running command: blastn -query GCF_008151785.1_ASM815178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b60da34-b1a2-4898-b376-95d17264e0f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008151785.1_ASM815178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:21,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:21,901] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:21,901] [INFO] Target genome list was writen to GCF_008151785.1_ASM815178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:21,920] [INFO] Task started: fastANI
[2024-01-24 13:46:21,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa50215-a013-4591-8c8b-1a6715b32b84/GCF_008151785.1_ASM815178v1_genomic.fna.gz --refList GCF_008151785.1_ASM815178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008151785.1_ASM815178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:30,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:30,351] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:30,351] [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_008151785.1	s__Peptacetobacter hiranonis	100.0	838	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	97.84	95.69	0.88	0.73	5	conclusive
GCA_900539645.1	s__Peptacetobacter sp900539645	94.1696	497	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	97.26	95.86	0.91	0.87	4	-
GCA_900550335.1	s__Peptacetobacter sp900550335	91.3988	413	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	99.93	99.93	0.85	0.85	2	-
GCF_006861675.1	s__Peptacetobacter hominis	80.3702	321	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012317385.1	s__GCA-900066495 sp900545985	79.5807	154	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	98.78	98.75	0.89	0.89	3	-
GCF_900015215.1	s__Romboutsia ilealis	79.071	151	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
GCF_900002575.1	s__Romboutsia_C hominis	78.8223	177	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCA_902362365.1	s__GCA-900066495 sp902362365	78.0147	146	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904418825.1	s__Romboutsia sp904418825	77.836	149	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	99.17	99.17	0.88	0.88	2	-
GCF_000808015.1	s__Terrisporobacter othiniensis	77.7859	153	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.48	99.45	0.91	0.90	3	-
GCF_002251085.2	s__Romboutsia_B maritimum	77.6135	148	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917235.1	s__Clostridioides_A sp002390935	77.1506	114	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A	95.0	96.42	96.30	0.91	0.89	4	-
GCF_002250835.2	s__Romboutsia_A weinsteinii	77.1285	166	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:30,353] [INFO] GTDB search result was written to GCF_008151785.1_ASM815178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:30,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:30,358] [INFO] DFAST_QC result json was written to GCF_008151785.1_ASM815178v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:30,358] [INFO] DFAST_QC completed!
[2024-01-24 13:46:30,358] [INFO] Total running time: 0h0m44s