[2024-01-24 12:31:05,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:05,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:05,173] [INFO] DQC Reference Directory: /var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference
[2024-01-24 12:31:06,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:06,527] [INFO] Task started: Prodigal
[2024-01-24 12:31:06,527] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfdd6f68-005b-4ff0-a77c-8a68db37f63c/GCF_003014595.1_ASM301459v1_genomic.fna.gz | prodigal -d GCF_003014595.1_ASM301459v1_genomic.fna/cds.fna -a GCF_003014595.1_ASM301459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:48,419] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:48,419] [INFO] Task started: HMMsearch
[2024-01-24 12:31:48,419] [INFO] Running command: hmmsearch --tblout GCF_003014595.1_ASM301459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference/reference_markers.hmm GCF_003014595.1_ASM301459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:48,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:48,807] [INFO] Found 6/6 markers.
[2024-01-24 12:31:48,876] [INFO] Query marker FASTA was written to GCF_003014595.1_ASM301459v1_genomic.fna/markers.fasta
[2024-01-24 12:31:48,876] [INFO] Task started: Blastn
[2024-01-24 12:31:48,877] [INFO] Running command: blastn -query GCF_003014595.1_ASM301459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference/reference_markers.fasta -out GCF_003014595.1_ASM301459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:49,474] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:49,478] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:49,478] [INFO] Target genome list was writen to GCF_003014595.1_ASM301459v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:49,485] [INFO] Task started: fastANI
[2024-01-24 12:31:49,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfdd6f68-005b-4ff0-a77c-8a68db37f63c/GCF_003014595.1_ASM301459v1_genomic.fna.gz --refList GCF_003014595.1_ASM301459v1_genomic.fna/target_genomes.txt --output GCF_003014595.1_ASM301459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:06,197] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:06,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:06,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:06,211] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:06,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:06,212] [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
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	100.0	2805	2807	95	conclusive
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	88.6626	2324	2807	95	below_threshold
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	81.2159	1342	2807	95	below_threshold
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	80.799	1242	2807	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	80.439	1102	2807	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	79.7711	982	2807	95	below_threshold
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	77.5924	388	2807	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	77.5056	353	2807	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	77.5025	365	2807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:06,213] [INFO] DFAST Taxonomy check result was written to GCF_003014595.1_ASM301459v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:06,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:06,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:06,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference/checkm_data
[2024-01-24 12:32:06,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:06,291] [INFO] Task started: CheckM
[2024-01-24 12:32:06,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014595.1_ASM301459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014595.1_ASM301459v1_genomic.fna/checkm_input GCF_003014595.1_ASM301459v1_genomic.fna/checkm_result
[2024-01-24 12:33:53,789] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:53,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:53,820] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:53,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:53,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014595.1_ASM301459v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:53,821] [INFO] Task started: Blastn
[2024-01-24 12:33:53,822] [INFO] Running command: blastn -query GCF_003014595.1_ASM301459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge324bc33-daba-47d1-8b2a-14c36990f5e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014595.1_ASM301459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:54,609] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:54,613] [INFO] Selected 6 target genomes.
[2024-01-24 12:33:54,614] [INFO] Target genome list was writen to GCF_003014595.1_ASM301459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:54,623] [INFO] Task started: fastANI
[2024-01-24 12:33:54,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfdd6f68-005b-4ff0-a77c-8a68db37f63c/GCF_003014595.1_ASM301459v1_genomic.fna.gz --refList GCF_003014595.1_ASM301459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014595.1_ASM301459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:07,290] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:07,299] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:07,299] [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_003014595.1	s__Chitinophaga ginsengisoli	100.0	2805	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900102545.1	s__Chitinophaga filiformis	88.6676	2323	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142925.1	s__Chitinophaga sp900142925	87.5299	2263	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467415.1	s__Chitinophaga sp016467415	85.863	2194	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182155.1	s__Chitinophaga sp003182155	83.5441	1731	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168105.1	s__Chitinophaga sp902168105	83.5179	1751	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:07,301] [INFO] GTDB search result was written to GCF_003014595.1_ASM301459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:07,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:07,304] [INFO] DFAST_QC result json was written to GCF_003014595.1_ASM301459v1_genomic.fna/dqc_result.json
[2024-01-24 12:34:07,304] [INFO] DFAST_QC completed!
[2024-01-24 12:34:07,304] [INFO] Total running time: 0h3m2s