[2024-01-24 14:06:14,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference
[2024-01-24 14:06:16,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:16,118] [INFO] Task started: Prodigal
[2024-01-24 14:06:16,119] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6d86b88-142e-4354-9667-954cca8e7c5e/GCF_014641595.1_ASM1464159v1_genomic.fna.gz | prodigal -d GCF_014641595.1_ASM1464159v1_genomic.fna/cds.fna -a GCF_014641595.1_ASM1464159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:59,477] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:59,478] [INFO] Task started: HMMsearch
[2024-01-24 14:06:59,478] [INFO] Running command: hmmsearch --tblout GCF_014641595.1_ASM1464159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference/reference_markers.hmm GCF_014641595.1_ASM1464159v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:59,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:59,880] [INFO] Found 6/6 markers.
[2024-01-24 14:06:59,945] [INFO] Query marker FASTA was written to GCF_014641595.1_ASM1464159v1_genomic.fna/markers.fasta
[2024-01-24 14:06:59,945] [INFO] Task started: Blastn
[2024-01-24 14:06:59,945] [INFO] Running command: blastn -query GCF_014641595.1_ASM1464159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference/reference_markers.fasta -out GCF_014641595.1_ASM1464159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:00,545] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:00,551] [INFO] Selected 9 target genomes.
[2024-01-24 14:07:00,552] [INFO] Target genome list was writen to GCF_014641595.1_ASM1464159v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:00,567] [INFO] Task started: fastANI
[2024-01-24 14:07:00,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d86b88-142e-4354-9667-954cca8e7c5e/GCF_014641595.1_ASM1464159v1_genomic.fna.gz --refList GCF_014641595.1_ASM1464159v1_genomic.fna/target_genomes.txt --output GCF_014641595.1_ASM1464159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:14,214] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:14,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:14,231] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:14,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:14,231] [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
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	100.0	2620	2621	95	conclusive
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	84.4173	1889	2621	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	84.323	1873	2621	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	83.0402	1486	2621	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	82.9126	1614	2621	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	82.8778	1630	2621	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	77.6486	468	2621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,233] [INFO] DFAST Taxonomy check result was written to GCF_014641595.1_ASM1464159v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:14,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:14,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:14,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference/checkm_data
[2024-01-24 14:07:14,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:14,310] [INFO] Task started: CheckM
[2024-01-24 14:07:14,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641595.1_ASM1464159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641595.1_ASM1464159v1_genomic.fna/checkm_input GCF_014641595.1_ASM1464159v1_genomic.fna/checkm_result
[2024-01-24 14:09:04,200] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:04,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:04,228] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:04,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:04,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641595.1_ASM1464159v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:04,230] [INFO] Task started: Blastn
[2024-01-24 14:09:04,230] [INFO] Running command: blastn -query GCF_014641595.1_ASM1464159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48e0c75e-1331-4d7a-98fb-ae3b5a4560d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641595.1_ASM1464159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:05,071] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:05,084] [INFO] Selected 7 target genomes.
[2024-01-24 14:09:05,084] [INFO] Target genome list was writen to GCF_014641595.1_ASM1464159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:05,100] [INFO] Task started: fastANI
[2024-01-24 14:09:05,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d86b88-142e-4354-9667-954cca8e7c5e/GCF_014641595.1_ASM1464159v1_genomic.fna.gz --refList GCF_014641595.1_ASM1464159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641595.1_ASM1464159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:18,082] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:18,092] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:18,092] [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_014641595.1	s__Dyadobacter endophyticus	100.0	2620	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109045.1	s__Dyadobacter sp900109045	84.8214	1912	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014695.1	s__Dyadobacter jiangsuensis	84.4093	1891	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	84.3283	1872	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744695.1	s__Dyadobacter sp017744695	83.8511	1840	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	83.433	1641	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_000023125.1	s__Dyadobacter fermentans	83.0386	1486	2621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:18,094] [INFO] GTDB search result was written to GCF_014641595.1_ASM1464159v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:18,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:18,096] [INFO] DFAST_QC result json was written to GCF_014641595.1_ASM1464159v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:18,097] [INFO] DFAST_QC completed!
[2024-01-24 14:09:18,097] [INFO] Total running time: 0h3m3s