[2023-06-18 20:56:39,131] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:39,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:39,133] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference
[2023-06-18 20:56:40,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:40,327] [INFO] Task started: Prodigal
[2023-06-18 20:56:40,328] [INFO] Running command: gunzip -c /var/lib/cwl/stgc46eea30-8342-43fb-9097-726b30f9ec5c/GCA_018059285.1_ASM1805928v1_genomic.fna.gz | prodigal -d GCA_018059285.1_ASM1805928v1_genomic.fna/cds.fna -a GCA_018059285.1_ASM1805928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:42,946] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:42,947] [INFO] Task started: HMMsearch
[2023-06-18 20:56:42,947] [INFO] Running command: hmmsearch --tblout GCA_018059285.1_ASM1805928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference/reference_markers.hmm GCA_018059285.1_ASM1805928v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:43,109] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:43,111] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc46eea30-8342-43fb-9097-726b30f9ec5c/GCA_018059285.1_ASM1805928v1_genomic.fna.gz]
[2023-06-18 20:56:43,126] [INFO] Query marker FASTA was written to GCA_018059285.1_ASM1805928v1_genomic.fna/markers.fasta
[2023-06-18 20:56:43,126] [INFO] Task started: Blastn
[2023-06-18 20:56:43,126] [INFO] Running command: blastn -query GCA_018059285.1_ASM1805928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference/reference_markers.fasta -out GCA_018059285.1_ASM1805928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:43,606] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:43,610] [INFO] Selected 8 target genomes.
[2023-06-18 20:56:43,610] [INFO] Target genome list was writen to GCA_018059285.1_ASM1805928v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:43,614] [INFO] Task started: fastANI
[2023-06-18 20:56:43,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46eea30-8342-43fb-9097-726b30f9ec5c/GCA_018059285.1_ASM1805928v1_genomic.fna.gz --refList GCA_018059285.1_ASM1805928v1_genomic.fna/target_genomes.txt --output GCA_018059285.1_ASM1805928v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:47,686] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:47,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:47,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:47,697] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 20:56:47,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 20:56:47,698] [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 massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	99.1272	310	322	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.8083	131	322	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.6857	132	322	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	79.3702	106	322	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.364	139	322	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.0311	113	322	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.9495	111	322	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.6446	94	322	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:56:47,700] [INFO] DFAST Taxonomy check result was written to GCA_018059285.1_ASM1805928v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:47,700] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:47,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:47,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference/checkm_data
[2023-06-18 20:56:47,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:47,717] [INFO] Task started: CheckM
[2023-06-18 20:56:47,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018059285.1_ASM1805928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018059285.1_ASM1805928v1_genomic.fna/checkm_input GCA_018059285.1_ASM1805928v1_genomic.fna/checkm_result
[2023-06-18 20:57:02,805] [INFO] Task succeeded: CheckM
[2023-06-18 20:57:02,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:57:02,822] [INFO] ===== Completeness check finished =====
[2023-06-18 20:57:02,822] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:57:02,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018059285.1_ASM1805928v1_genomic.fna/markers.fasta)
[2023-06-18 20:57:02,823] [INFO] Task started: Blastn
[2023-06-18 20:57:02,823] [INFO] Running command: blastn -query GCA_018059285.1_ASM1805928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8ca795d-73a8-44e3-b8be-944cb81b2df1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018059285.1_ASM1805928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:57:03,300] [INFO] Task succeeded: Blastn
[2023-06-18 20:57:03,304] [INFO] Selected 6 target genomes.
[2023-06-18 20:57:03,304] [INFO] Target genome list was writen to GCA_018059285.1_ASM1805928v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:57:03,307] [INFO] Task started: fastANI
[2023-06-18 20:57:03,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46eea30-8342-43fb-9097-726b30f9ec5c/GCA_018059285.1_ASM1805928v1_genomic.fna.gz --refList GCA_018059285.1_ASM1805928v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018059285.1_ASM1805928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:57:06,694] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:06,701] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:57:06,701] [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_001487165.1	s__Blautia_A massiliensis	99.1272	310	322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.95	95.87	0.85	0.71	55	conclusive
GCF_013304735.1	s__Blautia_A sp900066205	90.4017	296	322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_003461955.1	s__Blautia_A sp900066335	90.1133	295	322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCF_003474435.1	s__Blautia_A sp003474435	88.2863	280	322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.79	98.21	0.92	0.87	5	-
GCF_013304825.1	s__Blautia_A schinkii	88.247	282	322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCA_900764225.1	s__Blautia_A sp900764225	85.4613	241	322	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	-
--------------------------------------------------------------------------------
[2023-06-18 20:57:06,703] [INFO] GTDB search result was written to GCA_018059285.1_ASM1805928v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:57:06,703] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:57:06,706] [INFO] DFAST_QC result json was written to GCA_018059285.1_ASM1805928v1_genomic.fna/dqc_result.json
[2023-06-18 20:57:06,706] [INFO] DFAST_QC completed!
[2023-06-18 20:57:06,707] [INFO] Total running time: 0h0m28s