[2023-03-16 18:55:24,895] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:55:24,895] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:55:24,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference
[2023-03-16 18:55:26,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:55:26,750] [INFO] Task started: Prodigal
[2023-03-16 18:55:26,751] [INFO] Running command: cat /var/lib/cwl/stgc1314e7f-c60b-4ceb-9e89-f6641586dbb8/OceanDNA-b4487.fa | prodigal -d OceanDNA-b4487/cds.fna -a OceanDNA-b4487/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:56:16,807] [INFO] Task succeeded: Prodigal
[2023-03-16 18:56:16,807] [INFO] Task started: HMMsearch
[2023-03-16 18:56:16,807] [INFO] Running command: hmmsearch --tblout OceanDNA-b4487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference/reference_markers.hmm OceanDNA-b4487/protein.faa > /dev/null
[2023-03-16 18:56:17,077] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:56:17,077] [INFO] Found 6/6 markers.
[2023-03-16 18:56:17,125] [INFO] Query marker FASTA was written to OceanDNA-b4487/markers.fasta
[2023-03-16 18:56:17,140] [INFO] Task started: Blastn
[2023-03-16 18:56:17,140] [INFO] Running command: blastn -query OceanDNA-b4487/markers.fasta -db /var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference/reference_markers.fasta -out OceanDNA-b4487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:56:17,773] [INFO] Task succeeded: Blastn
[2023-03-16 18:56:17,774] [INFO] Selected 25 target genomes.
[2023-03-16 18:56:17,775] [INFO] Target genome list was writen to OceanDNA-b4487/target_genomes.txt
[2023-03-16 18:56:17,789] [INFO] Task started: fastANI
[2023-03-16 18:56:17,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1314e7f-c60b-4ceb-9e89-f6641586dbb8/OceanDNA-b4487.fa --refList OceanDNA-b4487/target_genomes.txt --output OceanDNA-b4487/fastani_result.tsv --threads 1
[2023-03-16 18:56:58,583] [INFO] Task succeeded: fastANI
[2023-03-16 18:56:58,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:56:58,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:56:58,593] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:56:58,593] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:56:58,594] [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
Arundinibacter roseus	strain=DMA-K-7a	GCA_004348825.1	2070510	2070510	type	True	76.9805	285	1760	95	below_threshold
Telluribacter humicola	strain=KCTC 42819	GCA_017355935.1	1720261	1720261	type	True	76.8176	196	1760	95	below_threshold
Persicitalea jodogahamensis	strain=KCTC 12866	GCA_014651615.1	402147	402147	type	True	76.5807	197	1760	95	below_threshold
Dyadobacter jejuensis	strain=DSM 100346	GCA_003149085.1	1082580	1082580	type	True	76.4726	66	1760	95	below_threshold
Rhabdobacter roseus	strain=DSM 105074	GCA_014202275.1	1655419	1655419	type	True	76.4284	192	1760	95	below_threshold
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	76.4091	66	1760	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	76.3468	64	1760	95	below_threshold
Dyadobacter tibetensis	strain=Y620-1	GCA_000566685.1	1211851	1211851	type	True	76.2669	63	1760	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	76.1795	80	1760	95	below_threshold
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	76.1031	66	1760	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	75.8042	80	1760	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	75.7015	58	1760	95	below_threshold
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	75.6862	58	1760	95	below_threshold
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	75.5134	65	1760	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	75.4236	58	1760	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:56:58,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4487/tc_result.tsv
[2023-03-16 18:56:58,594] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:56:58,594] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:56:58,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference/checkm_data
[2023-03-16 18:56:58,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:56:58,837] [INFO] Task started: CheckM
[2023-03-16 18:56:58,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4487/checkm_input OceanDNA-b4487/checkm_result
[2023-03-16 18:58:46,078] [INFO] Task succeeded: CheckM
[2023-03-16 18:58:46,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 18:58:46,092] [INFO] ===== Completeness check finished =====
[2023-03-16 18:58:46,092] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:58:46,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4487/markers.fasta)
[2023-03-16 18:58:46,093] [INFO] Task started: Blastn
[2023-03-16 18:58:46,093] [INFO] Running command: blastn -query OceanDNA-b4487/markers.fasta -db /var/lib/cwl/stgb347ba63-c67a-49f7-942b-9382749321d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:58:47,015] [INFO] Task succeeded: Blastn
[2023-03-16 18:58:47,019] [INFO] Selected 30 target genomes.
[2023-03-16 18:58:47,019] [INFO] Target genome list was writen to OceanDNA-b4487/target_genomes_gtdb.txt
[2023-03-16 18:58:47,089] [INFO] Task started: fastANI
[2023-03-16 18:58:47,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1314e7f-c60b-4ceb-9e89-f6641586dbb8/OceanDNA-b4487.fa --refList OceanDNA-b4487/target_genomes_gtdb.txt --output OceanDNA-b4487/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:59:24,347] [INFO] Task succeeded: fastANI
[2023-03-16 18:59:24,358] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:59:24,358] [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_004348825.1	s__Arundinibacter roseus	76.9897	284	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arundinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355935.1	s__Telluribacter humicola	76.8176	196	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Telluribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651615.1	s__Persicitalea jodogahamensis	76.5807	197	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Persicitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202275.1	s__Rhabdobacter roseus	76.4284	192	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rhabdobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014695.1	s__Dyadobacter jiangsuensis	76.4091	66	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	76.3468	64	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000566685.1	s__Dyadobacter tibetensis	76.2669	63	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167945.1	s__Dyadobacter psychrophilus	76.2616	59	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349265.1	s__Dyadobacter psychrotolerans	76.1795	80	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108855.1	s__Dyadobacter koreensis	76.1031	66	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	76.0583	85	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701505.1	s__Dyadobacter crusticola	75.8587	74	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641595.1	s__Dyadobacter endophyticus	75.8042	80	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727875.1	s__Larkinella sp008727875	75.7015	58	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003334855.1	s__Larkinella punicea	75.6862	58	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	75.6287	57	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259745.1	s__Larkinella arboricola	75.5134	65	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	75.4236	58	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:59:24,360] [INFO] GTDB search result was written to OceanDNA-b4487/result_gtdb.tsv
[2023-03-16 18:59:24,360] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:59:24,363] [INFO] DFAST_QC result json was written to OceanDNA-b4487/dqc_result.json
[2023-03-16 18:59:24,363] [INFO] DFAST_QC completed!
[2023-03-16 18:59:24,363] [INFO] Total running time: 0h3m59s