[2023-06-05 03:27:58,911] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:27:58,919] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:27:58,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference
[2023-06-05 03:28:00,810] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:28:00,811] [INFO] Task started: Prodigal
[2023-06-05 03:28:00,812] [INFO] Running command: gunzip -c /var/lib/cwl/stgc969fe64-d7bd-4252-aa4e-8201d9b757a0/GCA_902805495.1_AVDCRST-MAG54_genomic.fna.gz | prodigal -d GCA_902805495.1_AVDCRST-MAG54_genomic.fna/cds.fna -a GCA_902805495.1_AVDCRST-MAG54_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:28:10,304] [INFO] Task succeeded: Prodigal
[2023-06-05 03:28:10,305] [INFO] Task started: HMMsearch
[2023-06-05 03:28:10,305] [INFO] Running command: hmmsearch --tblout GCA_902805495.1_AVDCRST-MAG54_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference/reference_markers.hmm GCA_902805495.1_AVDCRST-MAG54_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:28:10,586] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:28:10,588] [INFO] Found 6/6 markers.
[2023-06-05 03:28:10,627] [INFO] Query marker FASTA was written to GCA_902805495.1_AVDCRST-MAG54_genomic.fna/markers.fasta
[2023-06-05 03:28:10,628] [INFO] Task started: Blastn
[2023-06-05 03:28:10,628] [INFO] Running command: blastn -query GCA_902805495.1_AVDCRST-MAG54_genomic.fna/markers.fasta -db /var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference/reference_markers.fasta -out GCA_902805495.1_AVDCRST-MAG54_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:12,277] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:12,281] [INFO] Selected 15 target genomes.
[2023-06-05 03:28:12,282] [INFO] Target genome list was writen to GCA_902805495.1_AVDCRST-MAG54_genomic.fna/target_genomes.txt
[2023-06-05 03:28:12,319] [INFO] Task started: fastANI
[2023-06-05 03:28:12,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgc969fe64-d7bd-4252-aa4e-8201d9b757a0/GCA_902805495.1_AVDCRST-MAG54_genomic.fna.gz --refList GCA_902805495.1_AVDCRST-MAG54_genomic.fna/target_genomes.txt --output GCA_902805495.1_AVDCRST-MAG54_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:28:32,159] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:32,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:28:32,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:28:32,175] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:28:32,175] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:28:32,175] [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
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	87.3879	965	1123	95	below_threshold
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	86.0106	964	1123	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	81.4798	778	1123	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	81.2133	759	1123	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	81.1867	762	1123	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	81.1593	775	1123	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	78.2403	578	1123	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	76.9905	453	1123	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	76.9856	478	1123	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	76.9763	531	1123	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	76.9139	444	1123	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	76.5461	379	1123	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.4825	346	1123	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	76.4361	397	1123	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.3139	382	1123	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:28:32,177] [INFO] DFAST Taxonomy check result was written to GCA_902805495.1_AVDCRST-MAG54_genomic.fna/tc_result.tsv
[2023-06-05 03:28:32,178] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:28:32,178] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:28:32,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference/checkm_data
[2023-06-05 03:28:32,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:28:32,221] [INFO] Task started: CheckM
[2023-06-05 03:28:32,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902805495.1_AVDCRST-MAG54_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902805495.1_AVDCRST-MAG54_genomic.fna/checkm_input GCA_902805495.1_AVDCRST-MAG54_genomic.fna/checkm_result
[2023-06-05 03:29:17,504] [INFO] Task succeeded: CheckM
[2023-06-05 03:29:17,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:29:17,530] [INFO] ===== Completeness check finished =====
[2023-06-05 03:29:17,530] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:29:17,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902805495.1_AVDCRST-MAG54_genomic.fna/markers.fasta)
[2023-06-05 03:29:17,531] [INFO] Task started: Blastn
[2023-06-05 03:29:17,531] [INFO] Running command: blastn -query GCA_902805495.1_AVDCRST-MAG54_genomic.fna/markers.fasta -db /var/lib/cwl/stg917778f1-b895-4cc2-8e9a-be7f1d679c68/dqc_reference/reference_markers_gtdb.fasta -out GCA_902805495.1_AVDCRST-MAG54_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:29:20,115] [INFO] Task succeeded: Blastn
[2023-06-05 03:29:20,120] [INFO] Selected 13 target genomes.
[2023-06-05 03:29:20,120] [INFO] Target genome list was writen to GCA_902805495.1_AVDCRST-MAG54_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:29:20,450] [INFO] Task started: fastANI
[2023-06-05 03:29:20,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgc969fe64-d7bd-4252-aa4e-8201d9b757a0/GCA_902805495.1_AVDCRST-MAG54_genomic.fna.gz --refList GCA_902805495.1_AVDCRST-MAG54_genomic.fna/target_genomes_gtdb.txt --output GCA_902805495.1_AVDCRST-MAG54_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:29:34,783] [INFO] Task succeeded: fastANI
[2023-06-05 03:29:34,796] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:29:34,797] [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_902805495.1	s__Actinomycetospora sp902805495	100.0	1104	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003096675.1	s__Actinomycetospora cinnamomea	87.4055	964	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363095.1	s__Actinomycetospora succinea	86.0099	964	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	81.6262	782	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	81.2223	758	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379625.1	s__Actinomycetospora chiangmaiensis	81.1757	763	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100955.1	s__Lentzea fradiae	77.0501	483	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025345.1	s__Geodermatophilus obscurus	76.9844	455	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	76.9134	444	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634695.1	s__Motilibacter peucedani	76.5321	384	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216915.1	s__Motilibacter rhizosphaerae	76.4587	394	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594885.1	s__Vallicoccus soli	76.3925	477	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Vallicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	75.9146	347	1123	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 03:29:34,799] [INFO] GTDB search result was written to GCA_902805495.1_AVDCRST-MAG54_genomic.fna/result_gtdb.tsv
[2023-06-05 03:29:34,799] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:29:34,803] [INFO] DFAST_QC result json was written to GCA_902805495.1_AVDCRST-MAG54_genomic.fna/dqc_result.json
[2023-06-05 03:29:34,803] [INFO] DFAST_QC completed!
[2023-06-05 03:29:34,803] [INFO] Total running time: 0h1m36s