[2024-01-24 13:17:31,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:31,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:31,016] [INFO] DQC Reference Directory: /var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference
[2024-01-24 13:17:32,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:32,293] [INFO] Task started: Prodigal
[2024-01-24 13:17:32,293] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1e6524b-2451-4817-a598-1492e660b4d1/GCF_004526345.1_ASM452634v1_genomic.fna.gz | prodigal -d GCF_004526345.1_ASM452634v1_genomic.fna/cds.fna -a GCF_004526345.1_ASM452634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:43,169] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:43,169] [INFO] Task started: HMMsearch
[2024-01-24 13:17:43,170] [INFO] Running command: hmmsearch --tblout GCF_004526345.1_ASM452634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference/reference_markers.hmm GCF_004526345.1_ASM452634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:43,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:43,445] [INFO] Found 6/6 markers.
[2024-01-24 13:17:43,477] [INFO] Query marker FASTA was written to GCF_004526345.1_ASM452634v1_genomic.fna/markers.fasta
[2024-01-24 13:17:43,478] [INFO] Task started: Blastn
[2024-01-24 13:17:43,478] [INFO] Running command: blastn -query GCF_004526345.1_ASM452634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference/reference_markers.fasta -out GCF_004526345.1_ASM452634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:44,691] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:44,694] [INFO] Selected 18 target genomes.
[2024-01-24 13:17:44,694] [INFO] Target genome list was writen to GCF_004526345.1_ASM452634v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:44,705] [INFO] Task started: fastANI
[2024-01-24 13:17:44,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e6524b-2451-4817-a598-1492e660b4d1/GCF_004526345.1_ASM452634v1_genomic.fna.gz --refList GCF_004526345.1_ASM452634v1_genomic.fna/target_genomes.txt --output GCF_004526345.1_ASM452634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:00,075] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:00,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:00,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:00,091] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:00,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:00,091] [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
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	100.0	1236	1237	95	conclusive
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	82.245	740	1237	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	82.2052	771	1237	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	82.195	791	1237	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	81.9581	703	1237	95	below_threshold
Ornithinimicrobium pratense	strain=W204	GCA_008843165.1	2593973	2593973	type	True	81.8272	736	1237	95	below_threshold
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	81.7658	744	1237	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	81.6472	689	1237	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	81.6462	712	1237	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	81.6136	669	1237	95	below_threshold
Serinicoccus profundi	strain=MCCC 1A05965	GCA_000224715.2	1078471	1078471	type	True	81.599	659	1237	95	below_threshold
Ornithinimicrobium avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	81.5944	738	1237	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	81.5675	696	1237	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	81.5675	680	1237	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	81.4862	677	1237	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	81.2027	657	1237	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.8288	519	1237	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	79.2074	355	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:00,093] [INFO] DFAST Taxonomy check result was written to GCF_004526345.1_ASM452634v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:00,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:00,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:00,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference/checkm_data
[2024-01-24 13:18:00,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:00,166] [INFO] Task started: CheckM
[2024-01-24 13:18:00,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004526345.1_ASM452634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004526345.1_ASM452634v1_genomic.fna/checkm_input GCF_004526345.1_ASM452634v1_genomic.fna/checkm_result
[2024-01-24 13:19:05,581] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:05,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:05,605] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:05,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:05,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004526345.1_ASM452634v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:05,607] [INFO] Task started: Blastn
[2024-01-24 13:19:05,607] [INFO] Running command: blastn -query GCF_004526345.1_ASM452634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6dedaa7-842c-4702-81b4-d38b5d025a0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004526345.1_ASM452634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:07,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:07,571] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:07,571] [INFO] Target genome list was writen to GCF_004526345.1_ASM452634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:07,576] [INFO] Task started: fastANI
[2024-01-24 13:19:07,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e6524b-2451-4817-a598-1492e660b4d1/GCF_004526345.1_ASM452634v1_genomic.fna.gz --refList GCF_004526345.1_ASM452634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004526345.1_ASM452634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:19,899] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,911] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:19,912] [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_004526345.1	s__Serinicoccus flavus	100.0	1236	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004322775.1	s__Serinicoccus sp004322775	82.4166	797	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	82.3686	763	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	82.2396	787	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	81.9751	704	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483745.1	s__Serinicoccus chungangensis_A	81.8433	710	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843165.1	s__Serinicoccus pratense	81.8239	732	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003702705.1	s__Ornithinimicrobium cerasi	81.7563	745	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	96.64	96.64	0.85	0.85	2	-
GCF_001685415.1	s__Serinicoccus hydrothermalis	81.6805	710	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001015.1	s__Serinicoccus profundi	81.6476	688	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.17	98.35	0.97	0.94	3	-
GCF_004153545.1	s__Serinicoccus sediminis	81.6101	670	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	81.5702	680	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	81.5645	696	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351765.1	s__Ornithinimicrobium sp003351765	81.5613	739	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577095.1	s__Ornithinimicrobium sp003577095	81.4464	556	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,915] [INFO] GTDB search result was written to GCF_004526345.1_ASM452634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:19,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:19,924] [INFO] DFAST_QC result json was written to GCF_004526345.1_ASM452634v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:19,924] [INFO] DFAST_QC completed!
[2024-01-24 13:19:19,924] [INFO] Total running time: 0h1m49s