[2024-01-25 17:45:05,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:05,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:05,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference
[2024-01-25 17:45:06,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:06,876] [INFO] Task started: Prodigal
[2024-01-25 17:45:06,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg39ed0f6f-359e-4a5b-b81c-dc0296dda6c9/GCF_002222595.2_ASM222259v2_genomic.fna.gz | prodigal -d GCF_002222595.2_ASM222259v2_genomic.fna/cds.fna -a GCF_002222595.2_ASM222259v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:13,016] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:13,017] [INFO] Task started: HMMsearch
[2024-01-25 17:45:13,017] [INFO] Running command: hmmsearch --tblout GCF_002222595.2_ASM222259v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference/reference_markers.hmm GCF_002222595.2_ASM222259v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:13,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:13,288] [INFO] Found 6/6 markers.
[2024-01-25 17:45:13,315] [INFO] Query marker FASTA was written to GCF_002222595.2_ASM222259v2_genomic.fna/markers.fasta
[2024-01-25 17:45:13,315] [INFO] Task started: Blastn
[2024-01-25 17:45:13,315] [INFO] Running command: blastn -query GCF_002222595.2_ASM222259v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference/reference_markers.fasta -out GCF_002222595.2_ASM222259v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:13,912] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:13,915] [INFO] Selected 14 target genomes.
[2024-01-25 17:45:13,915] [INFO] Target genome list was writen to GCF_002222595.2_ASM222259v2_genomic.fna/target_genomes.txt
[2024-01-25 17:45:13,926] [INFO] Task started: fastANI
[2024-01-25 17:45:13,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ed0f6f-359e-4a5b-b81c-dc0296dda6c9/GCF_002222595.2_ASM222259v2_genomic.fna.gz --refList GCF_002222595.2_ASM222259v2_genomic.fna/target_genomes.txt --output GCF_002222595.2_ASM222259v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:23,651] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:23,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:23,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:23,661] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:45:23,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:23,662] [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
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	100.0	1020	1021	95	conclusive
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	99.9986	1020	1021	95	conclusive
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	99.9768	1009	1021	95	conclusive
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	86.6531	169	1021	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	80.883	413	1021	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	80.7253	122	1021	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	79.467	174	1021	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.1719	75	1021	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.956	97	1021	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.7547	73	1021	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	78.6729	157	1021	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.8214	170	1021	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.7158	175	1021	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.7861	76	1021	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:23,663] [INFO] DFAST Taxonomy check result was written to GCF_002222595.2_ASM222259v2_genomic.fna/tc_result.tsv
[2024-01-25 17:45:23,664] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:23,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:23,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference/checkm_data
[2024-01-25 17:45:23,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:23,696] [INFO] Task started: CheckM
[2024-01-25 17:45:23,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002222595.2_ASM222259v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002222595.2_ASM222259v2_genomic.fna/checkm_input GCF_002222595.2_ASM222259v2_genomic.fna/checkm_result
[2024-01-25 17:45:46,839] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:46,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:46,860] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:46,860] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:46,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002222595.2_ASM222259v2_genomic.fna/markers.fasta)
[2024-01-25 17:45:46,861] [INFO] Task started: Blastn
[2024-01-25 17:45:46,861] [INFO] Running command: blastn -query GCF_002222595.2_ASM222259v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg629a5ad0-dd78-41a5-b18e-74e51ce11f1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002222595.2_ASM222259v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:47,917] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:47,920] [INFO] Selected 6 target genomes.
[2024-01-25 17:45:47,920] [INFO] Target genome list was writen to GCF_002222595.2_ASM222259v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:47,931] [INFO] Task started: fastANI
[2024-01-25 17:45:47,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ed0f6f-359e-4a5b-b81c-dc0296dda6c9/GCF_002222595.2_ASM222259v2_genomic.fna.gz --refList GCF_002222595.2_ASM222259v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002222595.2_ASM222259v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:52,184] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:52,190] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:52,190] [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_002222595.2	s__Blautia hansenii	100.0	1020	1021	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.38	97.55	0.86	0.75	11	conclusive
GCA_900539145.1	s__Blautia sp900539145	94.5667	697	1021	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.09	98.22	0.85	0.80	3	-
GCA_905201915.1	s__Blautia sp900555025	91.0618	600	1021	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.26	99.26	0.76	0.76	2	-
GCF_900120295.1	s__Blautia sp900120295	89.8716	712	1021	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547685.1	s__Blautia sp900547685	88.8056	582	1021	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013304445.1	s__Blautia sp900541955	81.2913	406	1021	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.45	99.32	0.89	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:52,191] [INFO] GTDB search result was written to GCF_002222595.2_ASM222259v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:52,192] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:52,195] [INFO] DFAST_QC result json was written to GCF_002222595.2_ASM222259v2_genomic.fna/dqc_result.json
[2024-01-25 17:45:52,195] [INFO] DFAST_QC completed!
[2024-01-25 17:45:52,195] [INFO] Total running time: 0h0m46s