[2023-06-05 01:31:30,465] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:31:30,467] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:31:30,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference
[2023-06-05 01:31:31,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:31:31,842] [INFO] Task started: Prodigal
[2023-06-05 01:31:31,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fade6a1-9b2e-4699-9bbd-4e82f16503da/GCA_004211475.1_ASM421147v1_genomic.fna.gz | prodigal -d GCA_004211475.1_ASM421147v1_genomic.fna/cds.fna -a GCA_004211475.1_ASM421147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:31:55,341] [INFO] Task succeeded: Prodigal
[2023-06-05 01:31:55,342] [INFO] Task started: HMMsearch
[2023-06-05 01:31:55,342] [INFO] Running command: hmmsearch --tblout GCA_004211475.1_ASM421147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference/reference_markers.hmm GCA_004211475.1_ASM421147v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:31:55,748] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:31:55,750] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3fade6a1-9b2e-4699-9bbd-4e82f16503da/GCA_004211475.1_ASM421147v1_genomic.fna.gz]
[2023-06-05 01:31:55,823] [INFO] Query marker FASTA was written to GCA_004211475.1_ASM421147v1_genomic.fna/markers.fasta
[2023-06-05 01:31:55,824] [INFO] Task started: Blastn
[2023-06-05 01:31:55,824] [INFO] Running command: blastn -query GCA_004211475.1_ASM421147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference/reference_markers.fasta -out GCA_004211475.1_ASM421147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:31:56,460] [INFO] Task succeeded: Blastn
[2023-06-05 01:31:56,465] [INFO] Selected 27 target genomes.
[2023-06-05 01:31:56,465] [INFO] Target genome list was writen to GCA_004211475.1_ASM421147v1_genomic.fna/target_genomes.txt
[2023-06-05 01:31:56,471] [INFO] Task started: fastANI
[2023-06-05 01:31:56,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fade6a1-9b2e-4699-9bbd-4e82f16503da/GCA_004211475.1_ASM421147v1_genomic.fna.gz --refList GCA_004211475.1_ASM421147v1_genomic.fna/target_genomes.txt --output GCA_004211475.1_ASM421147v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:32:18,672] [INFO] Task succeeded: fastANI
[2023-06-05 01:32:18,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:32:18,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:32:18,693] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:32:18,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:32:18,693] [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
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	80.5322	593	1237	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	80.4911	565	1237	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	79.9884	559	1237	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	79.4346	488	1237	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	78.6129	401	1237	95	below_threshold
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	77.8048	219	1237	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	77.2342	230	1237	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	77.2121	220	1237	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	77.2044	233	1237	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.1415	223	1237	95	below_threshold
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	76.9257	172	1237	95	below_threshold
Pedobacter helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	76.8944	209	1237	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	76.7658	181	1237	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	76.6323	185	1237	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	76.4119	106	1237	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	76.387	128	1237	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	76.2997	93	1237	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	76.2222	87	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:32:18,696] [INFO] DFAST Taxonomy check result was written to GCA_004211475.1_ASM421147v1_genomic.fna/tc_result.tsv
[2023-06-05 01:32:18,696] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:32:18,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:32:18,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference/checkm_data
[2023-06-05 01:32:18,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:32:18,766] [INFO] Task started: CheckM
[2023-06-05 01:32:18,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004211475.1_ASM421147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004211475.1_ASM421147v1_genomic.fna/checkm_input GCA_004211475.1_ASM421147v1_genomic.fna/checkm_result
[2023-06-05 01:33:24,832] [INFO] Task succeeded: CheckM
[2023-06-05 01:33:24,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 59.90%
Strain heterogeneity: 23.08%
--------------------------------------------------------------------------------
[2023-06-05 01:33:24,864] [INFO] ===== Completeness check finished =====
[2023-06-05 01:33:24,864] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:33:24,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004211475.1_ASM421147v1_genomic.fna/markers.fasta)
[2023-06-05 01:33:24,865] [INFO] Task started: Blastn
[2023-06-05 01:33:24,865] [INFO] Running command: blastn -query GCA_004211475.1_ASM421147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg447e4586-ca4e-4c0c-bcb7-12621fbe5333/dqc_reference/reference_markers_gtdb.fasta -out GCA_004211475.1_ASM421147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:33:25,592] [INFO] Task succeeded: Blastn
[2023-06-05 01:33:25,597] [INFO] Selected 21 target genomes.
[2023-06-05 01:33:25,597] [INFO] Target genome list was writen to GCA_004211475.1_ASM421147v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:33:25,765] [INFO] Task started: fastANI
[2023-06-05 01:33:25,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fade6a1-9b2e-4699-9bbd-4e82f16503da/GCA_004211475.1_ASM421147v1_genomic.fna.gz --refList GCA_004211475.1_ASM421147v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004211475.1_ASM421147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:33:40,812] [INFO] Task succeeded: fastANI
[2023-06-05 01:33:40,827] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 01:33:40,827] [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_005116505.1	s__Pedobacter sp005116505	80.5358	593	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	80.4807	566	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331645.1	s__Pedobacter sp004331645	79.9886	559	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295885.1	s__Pedobacter sp004295885	79.5122	356	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	79.4147	490	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204825.1	s__Pedobacter boryungensis	78.9834	420	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313325.1	s__Pedobacter namyangjuensis	78.6339	399	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377775.1	s__Pedobacter sp014377775	77.4368	241	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331675.1	s__Pedobacter sp004331675	77.2124	220	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215335.1	s__Pedobacter xixiisoli	77.1924	234	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003173595.1	s__Pedobacter yonginense	76.8983	174	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925325.1	s__Pedobacter helvus	76.8944	209	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	76.6323	185	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018492665.1	s__Pedobacter sp018492665	76.4621	126	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176505.1	s__Pedobacter nyackensis	76.3962	107	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266735.1	s__Pedobacter foliorum	76.387	128	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:33:40,829] [INFO] GTDB search result was written to GCA_004211475.1_ASM421147v1_genomic.fna/result_gtdb.tsv
[2023-06-05 01:33:40,830] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:33:40,838] [INFO] DFAST_QC result json was written to GCA_004211475.1_ASM421147v1_genomic.fna/dqc_result.json
[2023-06-05 01:33:40,838] [INFO] DFAST_QC completed!
[2023-06-05 01:33:40,838] [INFO] Total running time: 0h2m10s