[2023-06-30 23:56:36,907] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:56:36,909] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:56:36,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference
[2023-06-30 23:56:38,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:56:38,422] [INFO] Task started: Prodigal
[2023-06-30 23:56:38,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a3d20d5-8bb8-4301-8ec0-6d5650e07537/GCA_900765375.1_SRS294866_13_genomic.fna.gz | prodigal -d GCA_900765375.1_SRS294866_13_genomic.fna/cds.fna -a GCA_900765375.1_SRS294866_13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:56:44,945] [INFO] Task succeeded: Prodigal
[2023-06-30 23:56:44,946] [INFO] Task started: HMMsearch
[2023-06-30 23:56:44,946] [INFO] Running command: hmmsearch --tblout GCA_900765375.1_SRS294866_13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference/reference_markers.hmm GCA_900765375.1_SRS294866_13_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:56:45,231] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:56:45,232] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5a3d20d5-8bb8-4301-8ec0-6d5650e07537/GCA_900765375.1_SRS294866_13_genomic.fna.gz]
[2023-06-30 23:56:45,273] [INFO] Query marker FASTA was written to GCA_900765375.1_SRS294866_13_genomic.fna/markers.fasta
[2023-06-30 23:56:45,274] [INFO] Task started: Blastn
[2023-06-30 23:56:45,274] [INFO] Running command: blastn -query GCA_900765375.1_SRS294866_13_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference/reference_markers.fasta -out GCA_900765375.1_SRS294866_13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:56:45,791] [INFO] Task succeeded: Blastn
[2023-06-30 23:56:45,803] [INFO] Selected 13 target genomes.
[2023-06-30 23:56:45,803] [INFO] Target genome list was writen to GCA_900765375.1_SRS294866_13_genomic.fna/target_genomes.txt
[2023-06-30 23:56:45,804] [INFO] Task started: fastANI
[2023-06-30 23:56:45,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a3d20d5-8bb8-4301-8ec0-6d5650e07537/GCA_900765375.1_SRS294866_13_genomic.fna.gz --refList GCA_900765375.1_SRS294866_13_genomic.fna/target_genomes.txt --output GCA_900765375.1_SRS294866_13_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:56:53,147] [INFO] Task succeeded: fastANI
[2023-06-30 23:56:53,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:56:53,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:56:53,158] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:56:53,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 23:56:53,159] [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
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	92.9345	212	879	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	92.926	213	879	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	85.9486	290	879	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	85.8743	281	879	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	83.7422	256	879	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	81.4368	152	879	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	81.3334	151	879	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	80.2929	151	879	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	79.3271	76	879	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.1058	91	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 23:56:53,161] [INFO] DFAST Taxonomy check result was written to GCA_900765375.1_SRS294866_13_genomic.fna/tc_result.tsv
[2023-06-30 23:56:53,161] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:56:53,162] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:56:53,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference/checkm_data
[2023-06-30 23:56:53,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:56:53,199] [INFO] Task started: CheckM
[2023-06-30 23:56:53,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900765375.1_SRS294866_13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900765375.1_SRS294866_13_genomic.fna/checkm_input GCA_900765375.1_SRS294866_13_genomic.fna/checkm_result
[2023-06-30 23:57:19,847] [INFO] Task succeeded: CheckM
[2023-06-30 23:57:19,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:57:19,872] [INFO] ===== Completeness check finished =====
[2023-06-30 23:57:19,873] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:57:19,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900765375.1_SRS294866_13_genomic.fna/markers.fasta)
[2023-06-30 23:57:19,873] [INFO] Task started: Blastn
[2023-06-30 23:57:19,874] [INFO] Running command: blastn -query GCA_900765375.1_SRS294866_13_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b3f381-0e75-441f-8a61-7ca33917b37e/dqc_reference/reference_markers_gtdb.fasta -out GCA_900765375.1_SRS294866_13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:57:20,365] [INFO] Task succeeded: Blastn
[2023-06-30 23:57:20,370] [INFO] Selected 11 target genomes.
[2023-06-30 23:57:20,370] [INFO] Target genome list was writen to GCA_900765375.1_SRS294866_13_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:57:20,372] [INFO] Task started: fastANI
[2023-06-30 23:57:20,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a3d20d5-8bb8-4301-8ec0-6d5650e07537/GCA_900765375.1_SRS294866_13_genomic.fna.gz --refList GCA_900765375.1_SRS294866_13_genomic.fna/target_genomes_gtdb.txt --output GCA_900765375.1_SRS294866_13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:57:26,987] [INFO] Task succeeded: fastANI
[2023-06-30 23:57:26,998] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:57:26,998] [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_003471165.1	s__Blautia_A sp003471165	95.9812	323	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	conclusive
GCF_000169235.1	s__Dorea formicigenerans	92.9345	212	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_018919065.1	s__Blautia_A sp018919065	86.3667	248	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300825.1	s__Blautia_A wexlerae_B	85.9513	272	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_000484655.1	s__Blautia_A wexlerae	85.8159	283	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_009707925.1	s__Blautia_A luti	83.7061	257	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCA_905209435.1	s__Blautia_A sp905209435	83.385	212	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:57:27,000] [INFO] GTDB search result was written to GCA_900765375.1_SRS294866_13_genomic.fna/result_gtdb.tsv
[2023-06-30 23:57:27,001] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:57:27,006] [INFO] DFAST_QC result json was written to GCA_900765375.1_SRS294866_13_genomic.fna/dqc_result.json
[2023-06-30 23:57:27,006] [INFO] DFAST_QC completed!
[2023-06-30 23:57:27,006] [INFO] Total running time: 0h0m50s