[2024-01-25 19:57:50,648] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:50,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:50,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference
[2024-01-25 19:57:51,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:51,784] [INFO] Task started: Prodigal
[2024-01-25 19:57:51,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dbadb48-e968-46c1-ad2b-2e99cb9b9123/GCF_003352005.1_ASM335200v1_genomic.fna.gz | prodigal -d GCF_003352005.1_ASM335200v1_genomic.fna/cds.fna -a GCF_003352005.1_ASM335200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:59,174] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:59,174] [INFO] Task started: HMMsearch
[2024-01-25 19:57:59,174] [INFO] Running command: hmmsearch --tblout GCF_003352005.1_ASM335200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference/reference_markers.hmm GCF_003352005.1_ASM335200v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:59,413] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:59,414] [INFO] Found 6/6 markers.
[2024-01-25 19:57:59,447] [INFO] Query marker FASTA was written to GCF_003352005.1_ASM335200v1_genomic.fna/markers.fasta
[2024-01-25 19:57:59,447] [INFO] Task started: Blastn
[2024-01-25 19:57:59,448] [INFO] Running command: blastn -query GCF_003352005.1_ASM335200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference/reference_markers.fasta -out GCF_003352005.1_ASM335200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:59,996] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:00,000] [INFO] Selected 19 target genomes.
[2024-01-25 19:58:00,001] [INFO] Target genome list was writen to GCF_003352005.1_ASM335200v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:00,010] [INFO] Task started: fastANI
[2024-01-25 19:58:00,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dbadb48-e968-46c1-ad2b-2e99cb9b9123/GCF_003352005.1_ASM335200v1_genomic.fna.gz --refList GCF_003352005.1_ASM335200v1_genomic.fna/target_genomes.txt --output GCF_003352005.1_ASM335200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:14,555] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:14,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:14,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:14,566] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:14,566] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:14,566] [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
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	100.0	1366	1367	95	conclusive
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	87.0145	1027	1367	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	84.1934	914	1367	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.5552	73	1367	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	78.1731	194	1367	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	78.135	194	1367	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	78.128	235	1367	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	78.0939	250	1367	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	78.0562	253	1367	95	below_threshold
Oceanobacillus timonensis	strain=Marseille-P3532	GCA_900166635.1	1926285	1926285	type	True	78.0211	107	1367	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.6205	209	1367	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.6194	230	1367	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.0673	125	1367	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.0245	126	1367	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.9791	125	1367	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.918	121	1367	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	76.1833	61	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:14,567] [INFO] DFAST Taxonomy check result was written to GCF_003352005.1_ASM335200v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:14,568] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:14,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:14,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference/checkm_data
[2024-01-25 19:58:14,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:14,609] [INFO] Task started: CheckM
[2024-01-25 19:58:14,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003352005.1_ASM335200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003352005.1_ASM335200v1_genomic.fna/checkm_input GCF_003352005.1_ASM335200v1_genomic.fna/checkm_result
[2024-01-25 19:58:40,852] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:40,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:40,869] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:40,869] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:40,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003352005.1_ASM335200v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:40,870] [INFO] Task started: Blastn
[2024-01-25 19:58:40,870] [INFO] Running command: blastn -query GCF_003352005.1_ASM335200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ece04a4-5376-42cc-a3c5-f18131c5ea5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003352005.1_ASM335200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:41,649] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:41,652] [INFO] Selected 16 target genomes.
[2024-01-25 19:58:41,652] [INFO] Target genome list was writen to GCF_003352005.1_ASM335200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:41,663] [INFO] Task started: fastANI
[2024-01-25 19:58:41,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dbadb48-e968-46c1-ad2b-2e99cb9b9123/GCF_003352005.1_ASM335200v1_genomic.fna.gz --refList GCF_003352005.1_ASM335200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003352005.1_ASM335200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:55,954] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:55,964] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:55,964] [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_003352005.1	s__Oceanobacillus zhaokaii	100.0	1365	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	conclusive
GCF_003369565.1	s__Oceanobacillus chungangensis	87.0018	1029	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369575.1	s__Oceanobacillus arenosus	84.2036	912	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176885.1	s__Oceanobacillus senegalensis	78.1463	194	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618145.1	s__Oceanobacillus damuensis	78.137	198	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224365.1	s__Virgibacillus_F necropolis	78.0982	143	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008304605.1	s__Oceanobacillus polygoni	78.0627	237	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003515705.1	s__Oceanobacillus profundus	78.0481	252	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_900166635.1	s__Oceanobacillus timonensis	77.8744	106	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908155.1	s__Oceanobacillus caeni	77.8048	182	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_002287375.1	s__Virgibacillus_G profundi	77.6254	210	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003628445.1	s__Oceanobacillus bengalensis	77.5995	232	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873675.1	s__Lentibacillus litoralis	77.0673	125	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.9963	126	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_010993955.1	s__YIM-98839 sp010993955	76.9392	120	1367	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:55,966] [INFO] GTDB search result was written to GCF_003352005.1_ASM335200v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:55,966] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:55,969] [INFO] DFAST_QC result json was written to GCF_003352005.1_ASM335200v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:55,969] [INFO] DFAST_QC completed!
[2024-01-25 19:58:55,970] [INFO] Total running time: 0h1m5s