[2024-01-24 12:14:34,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,096] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference
[2024-01-24 12:14:35,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,318] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,319] [INFO] Running command: gunzip -c /var/lib/cwl/stg32b5cc08-ab55-43b6-870b-25e9e1e81fcb/GCF_003002875.1_ASM300287v1_genomic.fna.gz | prodigal -d GCF_003002875.1_ASM300287v1_genomic.fna/cds.fna -a GCF_003002875.1_ASM300287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:49,926] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:49,927] [INFO] Task started: HMMsearch
[2024-01-24 12:14:49,927] [INFO] Running command: hmmsearch --tblout GCF_003002875.1_ASM300287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference/reference_markers.hmm GCF_003002875.1_ASM300287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:50,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:50,229] [INFO] Found 6/6 markers.
[2024-01-24 12:14:50,279] [INFO] Query marker FASTA was written to GCF_003002875.1_ASM300287v1_genomic.fna/markers.fasta
[2024-01-24 12:14:50,279] [INFO] Task started: Blastn
[2024-01-24 12:14:50,279] [INFO] Running command: blastn -query GCF_003002875.1_ASM300287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference/reference_markers.fasta -out GCF_003002875.1_ASM300287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:50,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:50,827] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:50,827] [INFO] Target genome list was writen to GCF_003002875.1_ASM300287v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:50,832] [INFO] Task started: fastANI
[2024-01-24 12:14:50,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b5cc08-ab55-43b6-870b-25e9e1e81fcb/GCF_003002875.1_ASM300287v1_genomic.fna.gz --refList GCF_003002875.1_ASM300287v1_genomic.fna/target_genomes.txt --output GCF_003002875.1_ASM300287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:05,808] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:05,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:05,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:05,814] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:05,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:05,815] [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
Arcticibacter pallidicorallinus	strain=CGMCC 1.9313	GCA_003002875.1	1259464	1259464	type	True	100.0	1359	1360	95	conclusive
Arcticibacter eurypsychrophilus	strain=MJ9-5	GCA_001730525.1	1434752	1434752	type	True	78.2632	215	1360	95	below_threshold
Arcticibacter svalbardensis	strain=MN12-7	GCA_000403135.1	1288027	1288027	type	True	78.1919	212	1360	95	below_threshold
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	77.8196	99	1360	95	below_threshold
Pararcticibacter amylolyticus	strain=FJ4-8	GCA_003130405.1	2173175	2173175	type	True	77.4533	122	1360	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	76.9625	57	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,816] [INFO] DFAST Taxonomy check result was written to GCF_003002875.1_ASM300287v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:05,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:05,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:05,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference/checkm_data
[2024-01-24 12:15:05,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:05,860] [INFO] Task started: CheckM
[2024-01-24 12:15:05,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002875.1_ASM300287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002875.1_ASM300287v1_genomic.fna/checkm_input GCF_003002875.1_ASM300287v1_genomic.fna/checkm_result
[2024-01-24 12:15:49,001] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:49,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,038] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:49,038] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:49,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002875.1_ASM300287v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:49,039] [INFO] Task started: Blastn
[2024-01-24 12:15:49,039] [INFO] Running command: blastn -query GCF_003002875.1_ASM300287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4905343c-b5c8-417b-ae46-b078b984b9ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002875.1_ASM300287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:49,772] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:49,775] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:49,776] [INFO] Target genome list was writen to GCF_003002875.1_ASM300287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:49,786] [INFO] Task started: fastANI
[2024-01-24 12:15:49,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b5cc08-ab55-43b6-870b-25e9e1e81fcb/GCF_003002875.1_ASM300287v1_genomic.fna.gz --refList GCF_003002875.1_ASM300287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002875.1_ASM300287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:07,674] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:07,682] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:07,682] [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_003002875.1	s__Arcticibacter pallidicorallinus	100.0	1359	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001730525.1	s__Arcticibacter eurypsychrophilus	78.2632	215	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403135.1	s__Arcticibacter svalbardensis	78.1919	212	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716645.1	s__Pararcticibacter tournemirensis	77.8366	103	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	98.22	96.45	0.92	0.83	3	-
GCF_003130405.1	s__Pararcticibacter amylolyticus	77.4544	122	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355785.1	s__SYSU-D00535 sp017355785	77.197	98	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	77.045	55	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900564155.1	s__Pedobacter sp900564155	76.9756	55	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170795.1	s__Pedobacter sp000170795	76.9468	57	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355835.1	s__SYSU-D00535 sp017355835	76.902	96	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	76.7474	59	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:07,684] [INFO] GTDB search result was written to GCF_003002875.1_ASM300287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:07,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:07,687] [INFO] DFAST_QC result json was written to GCF_003002875.1_ASM300287v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:07,687] [INFO] DFAST_QC completed!
[2024-01-24 12:16:07,687] [INFO] Total running time: 0h1m34s