[2024-01-25 18:37:35,564] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:35,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:35,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference
[2024-01-25 18:37:36,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:36,653] [INFO] Task started: Prodigal
[2024-01-25 18:37:36,653] [INFO] Running command: gunzip -c /var/lib/cwl/stga8477b65-12f2-4198-ad2d-bde598cecda0/GCF_000258405.1_ASM25840v1_genomic.fna.gz | prodigal -d GCF_000258405.1_ASM25840v1_genomic.fna/cds.fna -a GCF_000258405.1_ASM25840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:42,930] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:42,931] [INFO] Task started: HMMsearch
[2024-01-25 18:37:42,931] [INFO] Running command: hmmsearch --tblout GCF_000258405.1_ASM25840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference/reference_markers.hmm GCF_000258405.1_ASM25840v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:43,151] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:43,152] [INFO] Found 6/6 markers.
[2024-01-25 18:37:43,184] [INFO] Query marker FASTA was written to GCF_000258405.1_ASM25840v1_genomic.fna/markers.fasta
[2024-01-25 18:37:43,184] [INFO] Task started: Blastn
[2024-01-25 18:37:43,184] [INFO] Running command: blastn -query GCF_000258405.1_ASM25840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference/reference_markers.fasta -out GCF_000258405.1_ASM25840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:43,715] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:43,718] [INFO] Selected 19 target genomes.
[2024-01-25 18:37:43,719] [INFO] Target genome list was writen to GCF_000258405.1_ASM25840v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:43,776] [INFO] Task started: fastANI
[2024-01-25 18:37:43,776] [INFO] Running command: fastANI --query /var/lib/cwl/stga8477b65-12f2-4198-ad2d-bde598cecda0/GCF_000258405.1_ASM25840v1_genomic.fna.gz --refList GCF_000258405.1_ASM25840v1_genomic.fna/target_genomes.txt --output GCF_000258405.1_ASM25840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:37:55,461] [INFO] Task succeeded: fastANI
[2024-01-25 18:37:55,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:37:55,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:37:55,466] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:37:55,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:37:55,466] [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
Ignavibacterium album	strain=JCM 16511	GCA_000258405.1	591197	591197	type	True	100.0	1216	1219	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:37:55,467] [INFO] DFAST Taxonomy check result was written to GCF_000258405.1_ASM25840v1_genomic.fna/tc_result.tsv
[2024-01-25 18:37:55,468] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:37:55,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:37:55,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference/checkm_data
[2024-01-25 18:37:55,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:37:55,509] [INFO] Task started: CheckM
[2024-01-25 18:37:55,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000258405.1_ASM25840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000258405.1_ASM25840v1_genomic.fna/checkm_input GCF_000258405.1_ASM25840v1_genomic.fna/checkm_result
[2024-01-25 18:38:19,349] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:19,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:19,366] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:19,367] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:19,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000258405.1_ASM25840v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:19,368] [INFO] Task started: Blastn
[2024-01-25 18:38:19,368] [INFO] Running command: blastn -query GCF_000258405.1_ASM25840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf4e3b1-92f6-4d6a-801f-6b91777bd576/dqc_reference/reference_markers_gtdb.fasta -out GCF_000258405.1_ASM25840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:20,138] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:20,142] [INFO] Selected 11 target genomes.
[2024-01-25 18:38:20,142] [INFO] Target genome list was writen to GCF_000258405.1_ASM25840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:20,153] [INFO] Task started: fastANI
[2024-01-25 18:38:20,154] [INFO] Running command: fastANI --query /var/lib/cwl/stga8477b65-12f2-4198-ad2d-bde598cecda0/GCF_000258405.1_ASM25840v1_genomic.fna.gz --refList GCF_000258405.1_ASM25840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000258405.1_ASM25840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:28,462] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:28,469] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:38:28,470] [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_000258405.1	s__Ignavibacterium album	100.0	1217	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016222975.1	s__Ignavibacterium album_C	81.2502	819	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011329055.1	s__Ignavibacterium album_B	80.8911	766	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011368355.1	s__Ignavibacterium album_A	80.3324	772	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050295.1	s__IGN3 sp002050295	76.6331	227	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	99.89	99.89	0.88	0.88	2	-
GCA_016707115.1	s__IGN3 sp016707115	76.5931	246	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	98.99	98.99	0.85	0.85	2	-
GCA_013388525.1	s__IGN2 sp013388525	76.5464	124	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388545.1	s__JACAFB01 sp013388545	76.4368	122	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__JACAFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335755.1	s__JAGXRK01 sp018335755	76.2359	184	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__JAGXRK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860115.1	s__IGN2 sp014860115	76.0499	130	1219	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:38:28,471] [INFO] GTDB search result was written to GCF_000258405.1_ASM25840v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:28,471] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:28,474] [INFO] DFAST_QC result json was written to GCF_000258405.1_ASM25840v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:28,474] [INFO] DFAST_QC completed!
[2024-01-25 18:38:28,474] [INFO] Total running time: 0h0m53s