[2024-01-25 18:50:50,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference
[2024-01-25 18:50:51,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,760] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d048330-775b-4c6f-977c-0081bcc4b3e8/GCF_016811075.1_ASM1681107v1_genomic.fna.gz | prodigal -d GCF_016811075.1_ASM1681107v1_genomic.fna/cds.fna -a GCF_016811075.1_ASM1681107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:12,240] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:12,240] [INFO] Task started: HMMsearch
[2024-01-25 18:51:12,240] [INFO] Running command: hmmsearch --tblout GCF_016811075.1_ASM1681107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference/reference_markers.hmm GCF_016811075.1_ASM1681107v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:12,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:12,489] [INFO] Found 6/6 markers.
[2024-01-25 18:51:12,522] [INFO] Query marker FASTA was written to GCF_016811075.1_ASM1681107v1_genomic.fna/markers.fasta
[2024-01-25 18:51:12,522] [INFO] Task started: Blastn
[2024-01-25 18:51:12,522] [INFO] Running command: blastn -query GCF_016811075.1_ASM1681107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference/reference_markers.fasta -out GCF_016811075.1_ASM1681107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:13,089] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:13,092] [INFO] Selected 26 target genomes.
[2024-01-25 18:51:13,092] [INFO] Target genome list was writen to GCF_016811075.1_ASM1681107v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:13,118] [INFO] Task started: fastANI
[2024-01-25 18:51:13,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d048330-775b-4c6f-977c-0081bcc4b3e8/GCF_016811075.1_ASM1681107v1_genomic.fna.gz --refList GCF_016811075.1_ASM1681107v1_genomic.fna/target_genomes.txt --output GCF_016811075.1_ASM1681107v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:31,296] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:31,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:31,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:31,304] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:51:31,304] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:51:31,304] [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
Oceaniferula marina	strain=N1E253	GCA_013391475.1	2748318	2748318	type	True	77.2579	158	1298	95	below_threshold
Sulfuriroseicoccus oceanibius	strain=T37	GCA_010681825.2	2707525	2707525	type	True	77.0704	52	1298	95	below_threshold
Persicirhabdus sediminis	strain=_KCTC 22039	GCA_016595495.1	454144	454144	type	True	76.9484	73	1298	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.7583	54	1298	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	76.67	90	1298	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.6592	88	1298	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.5526	82	1298	95	below_threshold
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	76.5159	73	1298	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.4393	94	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:31,306] [INFO] DFAST Taxonomy check result was written to GCF_016811075.1_ASM1681107v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:31,306] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:31,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:31,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference/checkm_data
[2024-01-25 18:51:31,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:31,349] [INFO] Task started: CheckM
[2024-01-25 18:51:31,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016811075.1_ASM1681107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016811075.1_ASM1681107v1_genomic.fna/checkm_input GCF_016811075.1_ASM1681107v1_genomic.fna/checkm_result
[2024-01-25 18:52:28,126] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:28,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:28,145] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:28,145] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:28,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016811075.1_ASM1681107v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:28,146] [INFO] Task started: Blastn
[2024-01-25 18:52:28,146] [INFO] Running command: blastn -query GCF_016811075.1_ASM1681107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg880a232f-6c7f-45d0-bd81-ca87673e62a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016811075.1_ASM1681107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:28,902] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:28,906] [INFO] Selected 18 target genomes.
[2024-01-25 18:52:28,906] [INFO] Target genome list was writen to GCF_016811075.1_ASM1681107v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:28,917] [INFO] Task started: fastANI
[2024-01-25 18:52:28,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d048330-775b-4c6f-977c-0081bcc4b3e8/GCF_016811075.1_ASM1681107v1_genomic.fna.gz --refList GCF_016811075.1_ASM1681107v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016811075.1_ASM1681107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:41,059] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:41,068] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:41,068] [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
GCA_016811075.1	s__UBA985 sp016811075	100.0	1297	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	conclusive
GCA_013041925.1	s__UBA985 sp013041925	77.413	206	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013391475.1	s__UBA985 sp013391475	77.2497	157	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010681825.2	s__JAAGVW01 sp010681825	77.0704	52	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__SLCJ01;g__JAAGVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292185.1	s__UBA985 sp002292185	76.8395	68	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	98.24	97.16	0.73	0.70	3	-
GCA_002304315.1	s__Haloferula sp002304315	76.7829	79	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018676385.1	s__UBA985 sp018676385	76.746	71	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003527555.1	s__UBA985 sp003527555	76.7064	73	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	98.70	97.71	0.76	0.72	4	-
GCA_017857425.1	s__UBA985 sp017857425	76.5981	98	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	96.59	96.59	0.83	0.83	2	-
GCF_014904755.1	s__Haloferula sp014904755	76.3176	104	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906515.1	s__Luteolibacter sp903906515	76.1547	57	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.85	99.81	0.93	0.92	3	-
GCA_905182475.1	s__Luteolibacter sp905182475	76.0783	54	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.83	99.83	0.94	0.94	2	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	75.6992	66	1298	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:41,069] [INFO] GTDB search result was written to GCF_016811075.1_ASM1681107v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:41,070] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:41,073] [INFO] DFAST_QC result json was written to GCF_016811075.1_ASM1681107v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:41,073] [INFO] DFAST_QC completed!
[2024-01-25 18:52:41,073] [INFO] Total running time: 0h1m50s