[2024-01-24 12:06:14,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference
[2024-01-24 12:06:15,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,803] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,804] [INFO] Running command: gunzip -c /var/lib/cwl/stg33535f03-bfb2-4e5f-88cf-eaf44922ffe7/GCF_003337355.1_ASM333735v1_genomic.fna.gz | prodigal -d GCF_003337355.1_ASM333735v1_genomic.fna/cds.fna -a GCF_003337355.1_ASM333735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:31,009] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:31,009] [INFO] Task started: HMMsearch
[2024-01-24 12:06:31,009] [INFO] Running command: hmmsearch --tblout GCF_003337355.1_ASM333735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference/reference_markers.hmm GCF_003337355.1_ASM333735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:31,391] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:31,393] [INFO] Found 6/6 markers.
[2024-01-24 12:06:31,439] [INFO] Query marker FASTA was written to GCF_003337355.1_ASM333735v1_genomic.fna/markers.fasta
[2024-01-24 12:06:31,439] [INFO] Task started: Blastn
[2024-01-24 12:06:31,439] [INFO] Running command: blastn -query GCF_003337355.1_ASM333735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference/reference_markers.fasta -out GCF_003337355.1_ASM333735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:32,078] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:32,081] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:32,082] [INFO] Target genome list was writen to GCF_003337355.1_ASM333735v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:32,088] [INFO] Task started: fastANI
[2024-01-24 12:06:32,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg33535f03-bfb2-4e5f-88cf-eaf44922ffe7/GCF_003337355.1_ASM333735v1_genomic.fna.gz --refList GCF_003337355.1_ASM333735v1_genomic.fna/target_genomes.txt --output GCF_003337355.1_ASM333735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:50,193] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:50,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:50,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:50,210] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:50,210] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:50,210] [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
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	79.2206	484	1802	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	79.1749	442	1802	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	78.935	555	1802	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	78.8213	491	1802	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	78.6379	567	1802	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.631	563	1802	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	78.5874	287	1802	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	78.567	535	1802	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	78.5058	464	1802	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	78.4278	365	1802	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	78.3456	377	1802	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	78.2819	218	1802	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	78.2616	471	1802	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	78.2614	335	1802	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	78.2492	365	1802	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	78.0657	327	1802	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	77.3248	110	1802	95	below_threshold
Paenibacillus sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	77.2862	111	1802	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.1358	73	1802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:50,212] [INFO] DFAST Taxonomy check result was written to GCF_003337355.1_ASM333735v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:50,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:50,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:50,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference/checkm_data
[2024-01-24 12:06:50,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:50,272] [INFO] Task started: CheckM
[2024-01-24 12:06:50,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337355.1_ASM333735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337355.1_ASM333735v1_genomic.fna/checkm_input GCF_003337355.1_ASM333735v1_genomic.fna/checkm_result
[2024-01-24 12:07:34,777] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:34,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:34,800] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:34,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:34,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337355.1_ASM333735v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:34,801] [INFO] Task started: Blastn
[2024-01-24 12:07:34,801] [INFO] Running command: blastn -query GCF_003337355.1_ASM333735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de524a0-d768-428f-8ab9-d9432c6321a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337355.1_ASM333735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:35,611] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:35,614] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:35,615] [INFO] Target genome list was writen to GCF_003337355.1_ASM333735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:35,623] [INFO] Task started: fastANI
[2024-01-24 12:07:35,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg33535f03-bfb2-4e5f-88cf-eaf44922ffe7/GCF_003337355.1_ASM333735v1_genomic.fna.gz --refList GCF_003337355.1_ASM333735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337355.1_ASM333735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:45,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:45,970] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:45,970] [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_003337355.1	s__Paenibacillus_A phaseoli	100.0	1801	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018403325.1	s__Paenibacillus_A vini	83.378	1103	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	83.0016	822	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084145.1	s__Paenibacillus_A faecis	80.1761	748	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	-
GCF_000455265.1	s__Paenibacillus_A antibioticophila	79.2147	484	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.82	95.80	0.91	0.82	4	-
GCF_003863965.1	s__Paenibacillus_A oralis	78.9288	554	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454495.1	s__Paenibacillus_A macerans	78.6301	567	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCF_014639155.1	s__Paenibacillus_A segetis	78.5461	291	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	78.232	474	1802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:45,972] [INFO] GTDB search result was written to GCF_003337355.1_ASM333735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:45,973] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:45,980] [INFO] DFAST_QC result json was written to GCF_003337355.1_ASM333735v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:45,980] [INFO] DFAST_QC completed!
[2024-01-24 12:07:45,980] [INFO] Total running time: 0h1m32s