[2024-01-24 14:05:53,622] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference
[2024-01-24 14:05:55,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,007] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,007] [INFO] Running command: gunzip -c /var/lib/cwl/stg84123968-4d3c-498c-ac79-6bf3aab6e60e/GCF_004103735.1_ASM410373v1_genomic.fna.gz | prodigal -d GCF_004103735.1_ASM410373v1_genomic.fna/cds.fna -a GCF_004103735.1_ASM410373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:02,035] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:02,035] [INFO] Task started: HMMsearch
[2024-01-24 14:06:02,035] [INFO] Running command: hmmsearch --tblout GCF_004103735.1_ASM410373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference/reference_markers.hmm GCF_004103735.1_ASM410373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:02,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:02,347] [INFO] Found 6/6 markers.
[2024-01-24 14:06:02,376] [INFO] Query marker FASTA was written to GCF_004103735.1_ASM410373v1_genomic.fna/markers.fasta
[2024-01-24 14:06:02,377] [INFO] Task started: Blastn
[2024-01-24 14:06:02,377] [INFO] Running command: blastn -query GCF_004103735.1_ASM410373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference/reference_markers.fasta -out GCF_004103735.1_ASM410373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:03,042] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:03,046] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:03,047] [INFO] Target genome list was writen to GCF_004103735.1_ASM410373v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:03,079] [INFO] Task started: fastANI
[2024-01-24 14:06:03,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg84123968-4d3c-498c-ac79-6bf3aab6e60e/GCF_004103735.1_ASM410373v1_genomic.fna.gz --refList GCF_004103735.1_ASM410373v1_genomic.fna/target_genomes.txt --output GCF_004103735.1_ASM410373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:12,917] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:12,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:12,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:12,924] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:12,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:12,925] [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
Aminipila luticellarii	strain=JN-18	GCA_004103735.1	2507160	2507160	type	True	100.0	916	916	95	conclusive
Aminipila terrae	strain=CBA3637	GCA_010120715.1	2697030	2697030	type	True	80.4863	437	916	95	below_threshold
Aminipila butyrica	strain=DSM 103574	GCA_010669305.1	433296	433296	type	True	79.0558	265	916	95	below_threshold
Sinanaerobacter chloroacetimidivorans	strain=BAD-6	GCA_018128545.1	2818044	2818044	type	True	78.2196	82	916	95	below_threshold
Anaerovorax odorimutans	strain=DSM 5092	GCA_000426305.1	109327	109327	type	True	76.7687	54	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:12,926] [INFO] DFAST Taxonomy check result was written to GCF_004103735.1_ASM410373v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:12,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:12,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:12,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference/checkm_data
[2024-01-24 14:06:12,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:12,963] [INFO] Task started: CheckM
[2024-01-24 14:06:12,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004103735.1_ASM410373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004103735.1_ASM410373v1_genomic.fna/checkm_input GCF_004103735.1_ASM410373v1_genomic.fna/checkm_result
[2024-01-24 14:06:39,531] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:39,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:39,552] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:39,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:39,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004103735.1_ASM410373v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:39,553] [INFO] Task started: Blastn
[2024-01-24 14:06:39,553] [INFO] Running command: blastn -query GCF_004103735.1_ASM410373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7bb10ba-399b-41e5-8b5f-cddda5d53acf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004103735.1_ASM410373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:40,383] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:40,386] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:40,386] [INFO] Target genome list was writen to GCF_004103735.1_ASM410373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:40,404] [INFO] Task started: fastANI
[2024-01-24 14:06:40,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg84123968-4d3c-498c-ac79-6bf3aab6e60e/GCF_004103735.1_ASM410373v1_genomic.fna.gz --refList GCF_004103735.1_ASM410373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004103735.1_ASM410373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:48,176] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:48,182] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:48,182] [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_004103735.1	s__Aminipila sp004103735	100.0	916	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010120715.1	s__Aminipila terrae	80.5453	440	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455605.1	s__Aminipila sp002455605	79.1663	291	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	99.31	99.31	0.92	0.92	2	-
GCF_010669305.1	s__Aminipila butyrica	79.1194	266	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255415.1	s__Aminipila aminobutyricum	77.8011	144	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:48,183] [INFO] GTDB search result was written to GCF_004103735.1_ASM410373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:48,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:48,186] [INFO] DFAST_QC result json was written to GCF_004103735.1_ASM410373v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:48,186] [INFO] DFAST_QC completed!
[2024-01-24 14:06:48,186] [INFO] Total running time: 0h0m55s